Contacts of the helix formed by residues 108 - 122 (chain B) in PDB entry 3EGC
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 ASP 108 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105B THR* 3.1 22.2 + - - +
106B ALA 4.2 3.1 - - - +
107B GLU* 1.3 77.2 - - - +
109B ILE* 1.3 60.1 + - - +
110B VAL* 3.1 22.6 + - - +
111B ARG* 3.2 34.2 + - - +
112B GLU* 3.0 22.7 + - - +
132B SER* 4.2 2.2 - - - -
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Residues in contact with ILE 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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107B GLU 3.8 4.2 + - - -
108B ASP* 1.3 74.7 + - - +
110B VAL* 1.3 69.6 + - + +
112B GLU* 3.6 18.6 - - - +
113B ARG* 3.0 38.8 + - - +
132B SER* 4.0 12.6 - - - +
133B GLU 3.9 12.8 + - - +
134B GLY* 4.1 10.8 - - - -
135B GLU 3.7 20.6 - - - +
136B HIS* 3.5 29.8 - - + +
138B TYR* 4.7 4.5 - - + -
133C GLU* 4.6 12.6 - - + +
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Residues in contact with VAL 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ASP* 3.1 18.4 + - - +
109B ILE* 1.3 82.1 - - + +
111B ARG* 1.3 60.0 + - + +
113B ARG* 3.6 29.2 + - - +
114B GLU* 3.1 44.7 + - + +
133C GLU* 5.8 0.4 - - - +
193C SER* 5.4 4.0 - - - +
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Residues in contact with ARG 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A GLU* 4.5 4.4 + - - -
91A SER* 5.1 11.6 + - - +
94A ARG* 2.2 52.7 + - - +
104B ASN* 2.9 28.7 + - - +
105B THR* 3.2 24.9 + - - +
106B ALA* 3.7 15.6 - - - +
108B ASP* 3.2 29.6 + - + +
110B VAL* 1.3 77.6 - - + +
112B GLU* 1.3 65.3 + - - +
114B GLU* 4.1 11.9 - - - +
115B ALA* 2.9 6.9 + - - +
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Residues in contact with GLU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ILE* 4.4 2.7 - - + -
105B THR* 3.5 20.8 - - + +
108B ASP 3.0 11.9 + - - +
109B ILE* 3.2 17.2 + - - +
111B ARG* 1.3 75.8 - - - +
113B ARG* 1.3 57.8 + - - +
115B ALA* 3.2 4.7 + - - +
116B VAL* 2.9 33.7 + - + +
129B LEU* 3.5 25.4 - - + +
130B ALA 4.4 0.3 - - - +
131B PRO* 3.3 9.5 - - - +
132B SER* 2.9 31.9 + - - +
136B HIS* 2.8 27.3 + - - -
138B TYR* 2.7 20.8 + - - +
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Residues in contact with ARG 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ILE* 3.0 32.7 + - - +
110B VAL* 3.7 29.5 - - - +
112B GLU* 1.3 77.1 - - - +
114B GLU* 1.3 62.7 + - + +
116B VAL* 3.5 1.7 + - - +
117B GLY* 3.1 19.9 + - - -
138B TYR* 3.7 55.1 + - + -
142B GLU* 5.0 3.6 - - - +
133C GLU* 4.0 12.9 + - - -
193C SER* 4.3 1.8 + - - +
194C ALA* 2.5 46.7 - - + +
195C GLY* 3.2 20.9 - - - +
224C ALA* 5.1 1.0 - - - +
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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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94A ARG* 3.7 14.6 + - - +
110B VAL* 3.1 31.9 + - + +
111B ARG* 3.2 15.8 + - - +
113B ARG* 1.3 79.3 - - + +
115B ALA* 1.3 58.0 + - - +
117B GLY* 3.5 1.1 + - - -
118B GLN* 2.9 33.0 + - - +
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Residues in contact with ALA 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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94A ARG* 3.2 18.5 - - - +
73B ILE* 3.8 16.2 - - + -
103B ALA* 3.7 28.0 - - + -
105B THR* 5.3 0.7 - - + -
111B ARG 2.9 9.5 + - - +
112B GLU* 3.7 4.7 - - - +
114B GLU* 1.3 75.0 - - - +
116B VAL* 1.3 55.4 + - - +
118B GLN* 3.5 9.4 - - - +
119B PHE* 2.7 42.3 + - + +
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Residues in contact with VAL 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ILE* 3.6 19.0 - - + +
112B GLU* 2.9 25.4 + - + +
113B ARG 3.7 4.9 - - - +
115B ALA* 1.3 75.7 - - - +
117B GLY* 1.3 58.8 + - - +
119B PHE* 3.9 1.1 - - - +
120B PHE* 2.8 29.5 + - - +
127B LEU* 4.0 16.7 - - + +
129B LEU* 5.1 4.0 - - + -
138B TYR* 3.4 25.6 - - + +
139B LEU* 3.9 11.4 - - + -
143B LEU* 3.7 35.4 - - + -
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Residues in contact with GLY 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 ARG 3.1 13.9 + - - -
114B GLU 3.9 2.2 - - - -
116B VAL* 1.3 77.9 - - - +
118B GLN* 1.3 51.2 + - - +
120B PHE* 3.8 6.4 - - - +
121B GLU* 2.8 41.6 + - - +
143B LEU* 6.1 0.7 - - - -
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Residues in contact with GLN 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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90A GLU* 5.9 0.6 + - - -
94A ARG* 4.4 24.2 + - - +
97A GLY 6.5 0.7 - - - -
98A TYR 4.7 5.4 + - - -
99A SER* 3.6 24.0 + - - +
102B LEU 5.8 0.2 + - - -
103B ALA* 5.4 2.4 - - - +
114B GLU* 2.9 20.8 + - - +
115B ALA* 3.5 8.2 - - - +
117B GLY* 1.3 75.7 - - - +
119B PHE* 1.3 86.9 + - + +
121B GLU* 2.9 33.6 - - - +
122B ARG* 3.2 15.9 + - + +
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Residues in contact with PHE 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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99A SER* 4.6 4.7 - - - -
100A VAL 5.7 0.4 - - - -
71B GLY* 3.5 19.1 - - - -
72B LEU 3.7 4.5 - - - -
73B ILE* 3.6 33.7 - - + -
101B LEU* 3.5 44.9 - - + -
102B LEU 3.6 15.0 - - - -
103B ALA* 3.6 19.7 - - + -
115B ALA 2.7 20.2 + - - +
116B VAL 4.0 0.9 - - - +
118B GLN* 1.3 101.2 - - + +
120B PHE* 1.3 62.5 + - - +
122B ARG* 3.2 14.5 + - - +
123B ARG 3.3 7.8 + - - -
124B VAL* 3.4 18.8 + - + +
127B LEU* 3.9 15.3 - - + -
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Residues in contact with PHE 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 VAL 2.8 19.3 + - - +
117B GLY* 3.8 5.8 - - - +
119B PHE* 1.3 76.1 - - - +
121B GLU* 1.3 56.5 + - + +
123B ARG* 2.7 74.2 + - - -
124B VAL* 4.4 5.4 - - - +
142B GLU 5.1 4.3 - - - -
143B LEU* 3.6 22.7 - - + -
144B PRO* 3.3 42.4 - - + -
147B PHE* 3.8 33.8 - + + -
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Residues in contact with GLU 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 GLY 2.8 33.0 + - - +
118B GLN* 2.9 28.3 - - - +
120B PHE* 1.3 74.8 - - + +
122B ARG* 1.3 71.2 + - - +
123B ARG* 2.9 23.1 + - - +
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Residues in contact with ARG 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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67A SER 3.1 24.5 + - - -
68A ASN* 3.1 24.9 + - - +
69A VAL* 3.5 20.2 - - - +
97A GLY 5.1 2.0 + - - -
99A SER* 2.7 26.8 + - - -
67B SER* 5.8 0.5 - - - -
101B LEU* 3.8 22.9 - - + -
118B GLN* 3.2 15.9 + - + +
119B PHE* 3.2 11.6 + - - +
120B PHE 3.1 1.2 - - - -
121B GLU* 1.3 85.1 + - - +
123B ARG* 1.3 68.8 + - - +
124B VAL* 3.4 1.8 + - - +
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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