Contacts of the helix formed by residues 103 - 116 (chain B) in PDB entry 5EJC
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 PRO 103 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B ALA 3.5 6.3 - - - +
102B THR* 1.4 89.5 - - + +
104B GLN* 1.3 64.2 + - - +
105B ALA* 3.3 6.7 - - + +
106B GLU* 3.2 33.1 + - + +
107B VAL* 3.0 19.2 + - - +
139B LYS* 6.4 1.8 - - - -
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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
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85B TYR* 3.3 24.9 + - - -
89B LEU* 6.0 1.0 - - - +
102B THR 3.7 2.8 + - - +
103B PRO* 1.3 73.3 - - - +
105B ALA* 1.3 57.3 + - - +
107B VAL* 3.2 17.7 + - - +
108B TYR* 3.0 64.0 + - + +
142B GLU* 3.4 22.1 + - + +
148B SER* 4.3 7.9 + - - +
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Residues in contact with ALA 105 (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 PRO* 3.3 4.8 - - + +
104B GLN* 1.3 78.0 - - - +
106B GLU* 1.3 58.1 + - - +
108B TYR* 3.5 13.2 + - - +
109B LEU* 3.1 20.8 + - - +
135B LEU* 3.3 20.6 - - + +
138B ALA* 4.1 12.8 - - + +
139B LYS* 3.7 34.3 - - + -
142B GLU* 3.8 12.8 + - - +
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Residues in contact with GLU 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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102B THR* 3.7 22.7 - - + +
103B PRO* 3.2 31.6 + - + +
105B ALA* 1.3 76.5 - - - +
107B VAL* 1.3 64.7 + - - +
109B LEU* 3.3 10.2 + - + +
110B ARG* 3.0 45.7 + - - +
123B PRO* 5.7 2.8 - - - +
127B LEU* 5.6 4.7 - - + -
135B LEU* 3.7 20.4 - - + +
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Residues in contact with VAL 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B TYR* 5.2 1.6 - - - +
89B LEU* 4.0 26.5 - - + -
92B LEU* 5.2 2.0 - - + -
98B VAL* 4.4 20.4 - - + -
99B SER 5.1 2.7 - - - +
102B THR* 4.3 20.0 - - - +
103B PRO 3.0 17.8 + - - +
104B GLN* 3.2 29.1 + - - +
106B GLU* 1.3 73.0 - - - +
108B TYR* 1.3 68.7 + - + +
110B ARG* 3.0 4.9 + - - +
111B MSE 2.9 35.8 + - + +
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Residues in contact with TYR 108 (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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85B TYR* 4.0 7.4 - - - -
104B GLN* 3.0 56.5 + - + +
105B ALA* 3.7 10.5 - - - +
106B GLU 3.4 0.2 - - - -
107B VAL* 1.3 77.7 - - + +
109B LEU* 1.3 56.7 + - - +
111B MSE 3.3 9.7 + - - +
112B TYR* 2.9 30.7 + - - +
134B PHE* 3.6 12.8 - - + -
138B ALA* 4.4 11.2 - - + -
142B GLU* 4.5 9.4 - - + +
148B SER* 3.2 39.8 + - - -
151B CYS* 3.8 27.4 - - + +
152B TYR* 3.6 36.8 - + + -
155B THR* 5.2 2.2 - - + -
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Residues in contact with LEU 109 (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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105B ALA 3.1 14.6 + - - +
106B GLU* 3.4 13.2 - - + +
108B TYR* 1.3 75.9 - - - +
110B ARG* 1.3 74.3 + - - +
112B TYR* 3.1 8.9 + - + +
113B GLN* 2.8 50.4 + - + +
127B LEU* 3.9 26.9 - - + -
131B ASP* 4.1 26.2 - - + +
134B PHE* 3.4 28.4 - - + -
135B LEU* 4.1 14.1 - - + -
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Residues in contact with ARG 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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92B LEU* 3.8 22.5 - - + +
97B PHE* 3.7 24.9 + - + +
98B VAL* 3.9 20.2 - - + -
106B GLU* 3.0 34.3 + - + +
107B VAL 3.0 7.2 + - - +
109B LEU* 1.3 88.4 - - - +
111B MSE 1.3 57.8 + - - +
113B GLN* 2.8 42.3 + - - +
114B LEU* 3.0 26.3 + - - +
119B LEU* 3.5 9.5 - - + +
120B PRO* 3.7 14.6 - - - +
122B SER 4.5 1.6 + - - -
123B PRO* 3.4 33.9 + - - +
125B PHE 4.7 5.5 + - - -
127B LEU* 5.2 12.3 - - - +
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Residues in contact with MSE 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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85B TYR* 3.2 65.1 - - + +
88B VAL* 3.6 27.0 - - + +
89B LEU* 4.0 5.8 - - - +
92B LEU* 3.6 17.7 - - + -
107B VAL* 2.9 32.0 + - + +
108B TYR* 3.5 8.5 - - - +
110B ARG* 1.3 72.7 - - - +
112B TYR* 1.3 61.6 + - - +
114B LEU* 3.3 2.3 + - - +
115B GLU* 2.9 33.8 + - - +
152B TYR* 3.5 28.5 - - + +
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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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108B TYR 2.9 17.5 + - - +
109B LEU* 3.4 10.8 - - + +
111B MSE 1.3 77.9 - - - +
113B GLN* 1.3 56.1 + - + +
115B GLU* 3.4 2.7 + - - +
116B SER* 2.6 54.2 + - - -
118B LYS* 4.9 15.5 + - + -
131B ASP* 5.9 2.5 - - - -
134B PHE* 3.4 44.6 - + + -
152B TYR* 3.5 10.3 + - + -
156B ARG* 3.8 35.7 - - + -
159B VAL* 4.1 7.5 - - + +
160B ASN* 5.2 8.7 + - + -
163B ASN* 3.9 20.1 + - - -
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Residues in contact with GLN 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B LEU* 2.8 28.4 + - + +
110B ARG* 2.8 44.6 + - - +
112B TYR* 1.3 79.9 - - + +
114B LEU* 1.3 52.0 + - - +
116B SER* 3.4 5.8 + - - -
117B GLY 2.8 14.2 + - - -
118B LYS* 2.8 50.7 + - + +
119B LEU* 3.8 7.9 - - + +
120B PRO* 3.4 19.8 - - - +
131B ASP* 3.3 34.1 + - - +
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Residues in contact with LEU 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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88B VAL* 3.5 36.1 - - + +
91B ALA* 4.5 3.6 - - + -
92B LEU* 4.5 7.9 - - + -
110B ARG 3.0 16.6 + - - +
111B MSE 3.6 4.5 - - - +
113B GLN* 1.3 77.1 - - - +
115B GLU* 1.3 62.3 + - - +
117B GLY* 3.1 11.9 + - - -
119B LEU* 4.0 17.4 - - + +
950D ALA 5.1 1.6 - - - +
953D ARG* 3.4 21.9 - - + +
954D ILE* 3.7 27.1 - - + +
957D VAL* 3.2 48.3 - - + +
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Residues in contact with GLU 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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84B GLN* 3.6 35.5 + - - +
88B VAL* 3.7 23.1 - - + +
111B MSE 2.9 18.1 + - - +
112B TYR* 3.9 4.0 - - - +
114B LEU* 1.3 77.8 - - + +
116B SER* 1.3 57.9 + - - +
117B GLY 3.3 0.4 - - - -
152B TYR* 3.0 31.8 + - - +
153B TRP* 4.8 1.8 - - - -
156B ARG* 3.1 38.1 + - - +
950D ALA* 4.9 4.5 - - + +
953D ARG* 3.7 21.7 + - - +
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Residues in contact with SER 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B TYR* 2.6 41.1 + - - -
113B GLN 3.6 2.8 + - - -
115B GLU* 1.3 75.7 - - - +
117B GLY* 1.3 61.9 + - - +
118B LYS* 3.5 30.7 + - - +
156B ARG* 5.8 3.4 - - - +
953D ARG* 4.3 10.9 + - - +
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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