Contacts of the helix formed by residues 102 - 124 (chain B) in PDB entry 3C5C
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 102 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ARG* 3.9 8.0 + - - -
99B SER* 3.0 21.3 + - - +
100B VAL 3.3 1.0 - - - -
101B ASP* 1.3 87.9 + - - +
103B ARG* 1.3 63.0 + - - +
104B GLN* 3.6 9.2 + - - +
105B SER* 3.0 30.6 + - - -
106B PHE* 3.2 15.2 + - - +
143B GLN* 3.3 4.7 - - - -
144B VAL* 4.0 1.3 - - - +
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Residues in contact with ARG 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B SER* 1.3 71.2 - - - +
104B GLN* 1.3 60.9 + - + +
106B PHE* 3.0 34.0 + - - +
107B ASP* 2.9 49.3 + - - +
143B GLN* 2.7 49.2 + - + +
144B VAL* 4.0 8.0 - - - +
148B GLU* 2.9 31.5 + - - -
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Residues in contact with GLN 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ARG* 3.9 25.8 - - - +
102B SER* 3.2 7.9 + - - +
103B ARG* 1.3 80.1 - - + +
105B SER* 1.3 61.9 + - - +
107B ASP* 3.3 9.0 + - - +
108B SER* 3.0 26.9 + - - -
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Residues in contact with SER 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ARG* 3.8 23.1 + - - +
29B ARG 6.2 0.2 - - - -
31B ALA* 3.6 14.7 - - - +
97B VAL 4.3 1.0 + - - +
98B TYR* 3.1 16.0 - - - +
99B SER* 3.0 27.0 + - - -
102B SER* 3.0 26.5 + - - -
104B GLN* 1.3 76.6 - - - +
106B PHE* 1.3 57.2 - - - +
108B SER* 3.5 3.6 + - - -
109B SER* 3.0 22.7 + - - -
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Residues in contact with PHE 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B TYR* 3.5 44.6 - + + +
102B SER 3.2 10.0 + - - +
103B ARG* 3.0 37.4 + - - +
105B SER* 1.3 77.2 - - - +
107B ASP* 1.3 71.3 + - - +
109B SER* 2.8 18.4 + - - -
110B SER* 3.4 4.9 + - - -
144B VAL* 3.7 23.8 - - + -
148B GLU* 3.4 30.7 - - + -
149B GLY* 4.1 1.3 - - - -
152B LEU* 3.4 36.2 - - + +
155B ARG* 6.1 1.6 - - - -
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Residues in contact with ASP 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B ARG* 2.9 41.1 + - - +
104B GLN* 3.7 10.4 - - - +
106B PHE* 1.3 81.2 - - - +
108B SER* 1.3 60.4 + - - +
110B SER* 2.6 28.1 + - - -
111B SER* 3.5 4.0 + - - -
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Residues in contact with SER 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ARG* 3.4 36.1 + - - +
79B ASP 5.6 2.0 + - - -
81B PRO* 6.5 0.4 - - - -
104B GLN 3.0 13.4 + - - -
105B SER 3.5 9.4 - - - -
107B ASP* 1.3 71.8 - - - +
109B SER* 1.3 66.6 + - - +
111B SER* 2.5 31.7 + - - -
112B TYR* 3.2 12.9 + - - -
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Residues in contact with SER 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B GLY* 5.6 0.4 - - - -
28B ARG 5.5 0.4 - - - +
96B VAL* 3.7 21.6 - - - +
97B VAL 4.3 4.9 - - - -
98B TYR* 3.8 20.5 - - - -
105B SER 3.0 14.3 + - - -
106B PHE 2.8 18.1 + - - -
107B ASP 3.3 0.2 - - - -
108B SER* 1.3 78.0 - - - +
110B SER* 1.3 60.4 + - - +
112B TYR* 3.2 8.2 + - - +
113B LEU* 3.1 26.8 + - - +
131B LEU* 3.8 6.8 - - - +
152B LEU* 3.4 15.8 - - - +
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Residues in contact with SER 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B PHE 3.4 4.0 + - - -
107B ASP* 2.6 23.8 + - - -
109B SER* 1.3 81.2 + - - +
111B SER* 1.3 57.4 + - - +
113B LEU* 3.3 6.3 + - - +
114B GLU* 2.9 35.5 + - - +
152B LEU* 3.8 28.7 - - - -
155B ARG* 4.4 16.1 + - - -
156B PHE* 3.9 2.5 - - - -
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Residues in contact with SER 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B PRO* 3.5 27.0 - - - +
107B ASP 3.5 3.1 + - - -
108B SER* 2.5 26.0 + - - -
110B SER* 1.3 83.4 + - - +
112B TYR* 1.3 55.5 + - - +
114B GLU* 3.5 8.1 + - - +
115B LEU* 3.1 28.1 + - - +
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Residues in contact with TYR 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B LEU* 3.8 29.8 - - + -
27B GLY* 3.5 39.5 + - - -
28B ARG* 3.9 5.1 - - - -
75B THR* 5.6 0.8 + - - -
77B ASP* 2.6 41.4 + - - +
79B ASP 4.9 3.9 + - - -
81B PRO* 3.6 26.6 - - + +
87B TYR* 3.8 8.1 - - - -
96B VAL* 3.8 17.0 - - + -
108B SER* 3.2 25.8 + - - -
109B SER* 3.2 8.7 + - - +
111B SER* 1.3 80.2 + - - +
113B LEU* 1.3 59.4 + - - +
115B LEU* 3.2 16.2 - - + +
116B LEU* 2.9 35.2 + - - +
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Residues in contact with LEU 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B VAL* 4.0 23.8 - - + -
109B SER 3.1 18.4 + - - +
110B SER 3.7 4.3 - - - +
112B TYR* 1.3 75.2 - - - +
114B GLU* 1.3 55.9 + - - +
116B LEU* 3.4 7.5 + - + +
117B ALA* 2.9 29.1 + - - +
129B ALA* 4.1 15.5 - - + -
131B LEU* 4.1 21.5 - - + -
152B LEU* 4.1 15.9 - - + +
156B PHE* 3.6 42.5 - - + -
158B CYS* 4.0 26.5 - - + -
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Residues in contact with GLU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B SER* 2.9 25.9 + - - +
111B SER* 3.8 8.5 - - - +
112B TYR 3.3 0.2 - - - -
113B LEU* 1.3 72.1 - - - +
115B LEU* 1.3 53.1 + - - +
117B ALA* 3.2 6.9 + - - +
118B LEU* 2.8 51.6 + - + +
155B ARG* 4.4 9.5 + - - +
156B PHE* 3.4 26.9 - - + -
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Residues in contact with LEU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B LEU* 4.9 1.3 - - + -
81B PRO* 3.5 26.0 - - + -
84B CYS* 3.4 28.3 - - + -
87B TYR* 3.7 21.5 - - + +
88B LEU* 3.4 30.2 - - + +
111B SER 3.1 10.9 + - - +
112B TYR* 3.2 18.2 - - + +
114B GLU* 1.3 73.1 - - - +
116B LEU* 1.3 71.5 + - + +
118B LEU* 3.4 9.9 + - - +
119B HIS* 3.0 24.6 + - - +
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Residues in contact with LEU 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B LEU* 4.2 4.9 - - + -
88B LEU* 3.8 16.8 - - + -
94B PHE* 3.7 63.5 - - + -
96B VAL* 3.9 17.3 - - + -
112B TYR 2.9 21.9 + - - +
113B LEU* 3.6 9.6 - - + +
115B LEU* 1.3 78.4 - - + +
117B ALA* 1.3 63.2 + - - +
119B HIS* 3.4 2.1 + - - +
120B ALA* 3.1 24.3 + - - +
127B ILE 6.0 1.3 - - - +
129B ALA* 3.9 18.8 - - + -
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Residues in contact with ALA 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B LEU 2.9 18.1 + - - +
114B GLU* 3.4 11.0 - - - +
116B LEU* 1.3 74.3 - - - +
118B LEU* 1.3 69.2 + - + +
120B ALA* 3.4 6.4 + - - +
121B LYS* 3.1 22.9 + - - +
156B PHE* 4.3 13.7 - - + -
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Residues in contact with LEU 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B GLU* 2.8 35.6 + - + +
115B LEU* 3.8 7.6 - - - +
117B ALA* 1.3 71.3 - - + +
119B HIS* 1.3 62.9 + - - +
121B LYS* 3.2 8.5 + - + +
122B GLU* 3.0 38.7 + - + +
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Residues in contact with HIS 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A PHE* 5.4 0.2 - + - -
85B GLU* 5.0 7.7 + - + -
88B LEU* 3.5 52.6 + - + +
89B ASN* 2.8 35.8 + - - -
115B LEU 3.0 16.6 + - - +
116B LEU 3.7 4.0 - - - +
118B LEU* 1.3 76.7 - - - +
120B ALA* 1.3 59.3 + - - +
122B GLU* 3.1 11.3 + - - -
123B THR* 2.8 69.2 + - + +
125B ARG* 4.7 6.7 - - + -
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Residues in contact with ALA 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B LEU 3.1 14.0 + - - +
117B ALA* 3.6 10.3 - - - +
119B HIS* 1.3 75.1 - - - +
121B LYS* 1.3 58.9 + - - +
123B THR* 4.2 2.2 - - - -
124B GLN* 2.8 32.1 + - - +
125B ARG* 3.2 26.2 - - - +
126B SER* 5.4 1.3 - - - -
127B ILE 5.6 1.3 - - - +
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Residues in contact with LYS 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B ALA 3.1 13.1 + - - +
118B LEU* 3.2 11.6 + - + +
120B ALA* 1.3 78.2 - - - +
122B GLU* 1.3 63.4 + - + +
124B GLN* 4.3 9.4 + - - +
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Residues in contact with GLU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ARG* 5.3 9.5 - - - +
45A PHE 3.9 2.9 - - - +
46A ILE* 3.8 15.6 - - - +
118B LEU* 3.0 32.1 + - + +
119B HIS* 3.8 11.3 + - - +
121B LYS* 1.3 78.4 - - + +
123B THR* 1.3 65.0 + - + +
124B GLN* 5.5 0.4 - - - -
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Residues in contact with THR 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A PHE* 3.3 35.0 - - + +
46A ILE* 3.6 2.7 - - - -
47A SER* 2.8 33.8 + - - -
119B HIS* 2.8 54.2 + - + +
122B GLU* 1.3 82.5 - - + +
124B GLN* 1.3 65.9 + - - +
125B ARG* 3.1 21.3 + - - +
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Residues in contact with GLN 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ILE* 4.4 19.7 - - + -
47A SER* 3.6 1.8 - - - -
48A GLU* 3.8 30.7 - - + +
120B ALA 2.8 17.1 + - - +
121B LYS 4.3 7.4 + - - +
122B GLU 3.7 0.6 - - - +
123B THR* 1.3 80.0 - - - +
125B ARG* 1.3 61.2 + - - +
126B SER* 3.3 5.5 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il