Contacts of the helix formed by residues 102 - 124 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ARG* 3.8 7.4 + - - -
99A SER* 3.0 15.0 + - - +
100A VAL 3.3 1.8 - - - -
101A ASP* 1.3 87.2 - - - +
103A ARG* 1.3 63.4 + - - +
104A GLN* 3.6 10.7 - - - +
105A SER* 3.1 29.1 + - - -
106A PHE* 3.1 18.7 + - - +
143A GLN* 3.6 4.0 - - - +
144A VAL* 4.4 2.2 - - - -
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Residues in contact with ARG 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A SER* 1.3 71.5 - - - +
104A GLN* 1.3 56.7 + - - +
106A PHE* 3.1 24.8 + - - +
107A ASP* 2.8 59.4 + - - +
143A GLN* 2.8 49.6 + - + +
144A VAL* 3.9 15.7 - - - +
148A GLU* 2.9 33.5 + - - -
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Residues in contact with GLN 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ARG* 3.8 32.2 + - - +
102A SER* 3.6 8.9 + - - +
103A ARG* 1.3 79.6 - - - +
105A SER* 1.3 57.6 + - - +
107A ASP* 3.4 8.1 + - - +
108A SER* 2.9 35.5 + - - -
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Residues in contact with SER 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ARG* 3.9 22.6 + - - +
29A ARG 5.7 0.2 + - - -
31A ALA* 3.7 14.1 + - - +
97A VAL 4.8 0.9 - - - +
98A TYR* 3.3 14.8 - - - +
99A SER* 3.1 25.2 + - - -
102A SER* 3.1 26.5 + - - -
104A GLN* 1.3 77.7 - - - +
106A PHE* 1.3 60.3 + - - +
108A SER* 3.4 2.9 + - - -
109A SER* 2.9 23.4 + - - -
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Residues in contact with PHE 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A TYR* 3.5 43.7 - + + -
102A SER 3.1 3.8 + - - +
103A ARG* 3.4 38.1 - - - +
105A SER* 1.3 78.1 - - - +
107A ASP* 1.3 69.7 + - - +
109A SER* 2.5 22.2 + - - -
110A SER* 3.4 3.8 + - - -
144A VAL* 3.6 31.9 - - + -
148A GLU* 3.5 28.0 - - + -
149A GLY* 4.0 7.4 - - - -
152A LEU* 3.5 31.6 - - + +
155A ARG* 6.3 0.4 - - - -
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Residues in contact with ASP 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ARG* 2.8 45.8 + - - +
104A GLN* 3.7 7.9 + - - +
106A PHE* 1.3 81.7 - - - +
108A SER* 1.3 60.8 + - - +
110A SER* 2.7 28.4 + - - -
111A SER* 3.7 3.3 + - - -
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Residues in contact with SER 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ARG* 3.5 32.1 + - - +
104A GLN* 2.9 22.2 + - - -
105A SER 3.7 5.4 - - - -
107A ASP* 1.3 75.9 - - - +
109A SER* 1.3 61.1 + - - +
111A SER* 2.5 29.9 + - - -
112A TYR* 3.1 14.3 - - - -
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Residues in contact with SER 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A GLY* 5.7 0.2 - - - -
28A ARG 5.6 0.2 - - - +
96A VAL* 3.7 19.9 - - - +
97A VAL 4.5 4.0 - - - -
98A TYR* 3.9 22.7 - - - -
105A SER 2.9 14.6 + - - -
106A PHE* 2.5 21.5 + - - -
108A SER* 1.3 76.5 - - - +
110A SER* 1.3 60.0 + - - +
112A TYR* 3.2 14.7 + - - +
113A LEU* 3.2 21.0 + - - +
131A LEU* 4.0 2.2 - - - +
152A LEU* 3.4 16.5 - - - +
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Residues in contact with SER 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A PHE 3.4 2.0 + - - -
107A ASP* 2.7 22.8 + - - -
109A SER* 1.3 80.6 + - - +
111A SER* 1.3 58.0 + - - +
113A LEU* 3.3 6.0 + - - +
114A GLU* 2.9 39.2 + - - +
152A LEU* 3.8 31.0 - - - -
155A ARG* 4.5 12.2 + - - -
156A PHE* 3.8 3.5 - - - -
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Residues in contact with SER 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A ASP 3.7 2.7 + - - -
108A SER* 2.5 26.8 + - - -
110A SER* 1.3 80.3 + - - +
112A TYR* 1.3 68.5 + - - +
114A GLU* 3.2 14.0 + - - +
115A LEU* 3.0 28.1 + - - +
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Residues in contact with TYR 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A LEU* 4.0 21.8 - - + +
27A GLY* 3.4 44.0 + - - -
28A ARG* 3.6 8.9 + - - -
77A ASP* 3.2 30.0 + - - +
87A TYR* 4.7 11.2 - - - -
96A VAL* 3.8 17.3 - - + -
108A SER* 3.1 32.7 - - - -
109A SER* 3.2 9.9 + - - +
111A SER* 1.3 86.2 + - - +
113A LEU* 1.3 59.7 + - - +
115A LEU* 3.3 14.7 + - + +
116A LEU* 3.0 32.4 + - - +
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Residues in contact with LEU 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A VAL* 3.9 25.4 - - + -
109A SER 3.2 14.4 + - - +
110A SER* 3.6 6.7 - - - +
111A SER 3.3 0.2 - - - -
112A TYR* 1.3 75.4 - - - +
114A GLU* 1.3 64.4 + - - +
116A LEU* 3.4 13.3 + - + +
117A ALA* 3.0 23.0 + - - +
129A ALA* 4.5 6.3 - - + -
131A LEU* 4.3 10.3 - - + -
152A LEU* 4.0 24.2 - - + +
156A PHE* 3.6 41.4 - - + +
158A CYS* 4.0 26.9 - - + -
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Residues in contact with GLU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A SER* 2.9 28.0 + - - +
111A SER* 3.2 13.9 + - - +
113A LEU* 1.3 74.9 - - - +
115A LEU* 1.3 58.0 + - - +
117A ALA* 3.2 5.3 + - - +
118A LEU* 2.9 44.2 + - + +
155A ARG* 4.6 7.8 + - - -
156A PHE* 3.6 22.6 - - + -
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Residues in contact with LEU 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A LEU* 6.0 1.1 - - + -
84A CYS* 4.2 18.2 - - + -
87A TYR* 3.8 24.7 - - + +
88A LEU* 4.0 23.8 - - + -
111A SER 3.0 13.1 + - - +
112A TYR* 3.4 20.2 - - + +
114A GLU* 1.3 75.7 - - - +
116A LEU* 1.3 57.8 + - + +
118A LEU* 3.3 12.5 + - + +
119A HIS* 2.9 33.8 + - + +
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Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A LEU* 4.2 7.9 - - + -
88A LEU* 3.7 16.4 - - + -
94A PHE* 3.6 59.7 - - + -
96A VAL* 4.0 15.0 - - + -
112A TYR 3.0 17.1 + - - +
113A LEU* 3.7 11.2 - - + +
114A GLU 3.3 0.2 - - - -
115A LEU* 1.3 74.1 - - + +
117A ALA* 1.3 57.2 + - - +
119A HIS* 3.6 4.6 + - - +
120A ALA* 3.0 30.4 + - - +
127A ILE 5.7 2.0 - - - +
129A ALA* 3.8 23.1 - - + -
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Residues in contact with ALA 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A LEU 3.0 13.0 + - - +
114A GLU* 3.2 11.4 + - - +
116A LEU* 1.3 73.4 - - - +
118A LEU* 1.3 60.1 + - + +
120A ALA* 3.3 6.2 + - - +
121A LYS* 2.9 29.7 + - - +
156A PHE* 4.6 11.9 - - + -
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Residues in contact with LEU 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A GLU* 2.9 36.1 + - + +
115A LEU* 3.7 12.6 - - + +
117A ALA* 1.3 69.7 - - + +
119A HIS* 1.3 56.5 + - - +
121A LYS* 3.1 8.6 + - + +
122A GLU* 2.8 61.5 + - + +
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Residues in contact with HIS 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A GLU* 4.9 7.6 + - + -
88A LEU* 3.5 53.8 + - + +
89A ASN* 2.7 35.7 + - - -
115A LEU* 2.9 19.1 + - + +
116A LEU* 3.8 3.8 - - + +
118A LEU* 1.3 77.5 - - - +
120A ALA* 1.3 58.0 + - - +
122A GLU* 3.2 11.5 + - - -
123A THR* 2.9 64.4 + - + +
125A ARG* 4.3 9.1 - - + +
127A ILE* 5.2 3.6 - - + -
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Residues in contact with ALA 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A LEU 3.0 17.9 + - - +
117A ALA* 3.6 7.0 - - - +
118A LEU 3.3 0.2 - - - -
119A HIS* 1.3 77.0 - - - +
121A LYS* 1.3 56.3 + - - +
124A GLN* 2.8 34.0 + - - +
125A ARG 3.2 28.0 + - - +
126A SER* 4.9 4.3 - - - -
127A ILE 5.5 1.1 - - - +
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Residues in contact with LYS 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A ALA 2.9 13.2 + - - +
118A LEU* 3.4 13.7 - - + +
120A ALA* 1.3 78.2 - - - +
122A GLU* 1.3 63.7 + - + +
123A THR 3.7 0.2 + - - -
124A GLN* 4.2 7.7 + - - +
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Residues in contact with GLU 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A LEU* 2.8 48.1 + - + +
119A HIS* 3.2 10.3 + - - +
121A LYS* 1.3 76.6 - - + +
123A THR* 1.3 67.5 + - + +
124A GLN* 5.7 0.3 - - - +
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Residues in contact with THR 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ASN* 4.8 3.6 - - - +
119A HIS* 2.9 48.0 + - + +
122A GLU* 1.3 87.0 - - + +
124A GLN* 1.3 67.7 + - - +
125A ARG* 3.2 25.0 + - - +
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Residues in contact with GLN 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A ALA 2.8 17.8 + - - +
121A LYS 4.2 6.1 + - - +
122A GLU 3.7 1.0 - - - +
123A THR* 1.3 78.3 - - - +
125A ARG* 1.3 56.9 + - - -
126A SER* 3.1 11.4 + - - -
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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
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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