Contacts of the helix formed by residues 116 - 129 (chain B) in PDB entry 3Q2S
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 116 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A LYS* 5.1 9.1 + - - -
111B LEU* 4.3 2.0 - - - +
114B GLY 4.0 2.0 + - - -
115B GLU* 1.3 76.9 - - - +
117B GLU* 1.3 70.9 + - - +
118B VAL* 3.4 10.5 + - - +
119B GLU* 3.0 51.6 + - + +
120B GLY* 2.9 23.4 + - - -
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Residues in contact with GLU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 5.3 7.6 - - - +
34A GLU* 4.9 3.2 - - - +
78B ARG* 5.1 6.3 - - - +
80B VAL* 4.6 7.1 - - + +
111B LEU* 4.2 22.1 - - + +
115B GLU 3.7 1.6 + - - -
116B ASP* 1.3 79.6 + - - +
118B VAL* 1.3 60.4 + - + +
120B GLY* 3.7 0.9 - - - -
121B LEU* 2.9 26.6 + - - +
171B HIS* 5.1 4.2 - - - -
173B LYS* 3.0 48.2 + - + +
175B PHE* 3.8 20.2 - - + -
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Residues in contact with VAL 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 4.1 36.1 - - + -
116B ASP* 3.4 7.8 + - - +
117B GLU* 1.3 73.7 - - + +
119B GLU* 1.3 61.6 + - + +
121B LEU* 2.7 28.2 + - - +
122B LYS* 2.9 30.3 + - - +
141B ILE* 3.9 37.0 - - + +
175B PHE* 4.6 8.3 - - + -
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Residues in contact with GLU 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B GLU* 4.6 2.8 - - + +
116B ASP* 3.0 35.6 + - + +
118B VAL* 1.3 77.8 - - + +
120B GLY* 1.3 64.3 + - - +
122B LYS* 3.3 12.6 + - + +
123B ARG* 3.1 21.0 + - - +
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Residues in contact with GLY 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B LEU* 4.0 3.6 - - - -
115B GLU* 3.2 29.5 + - - +
116B ASP 2.9 19.1 + - - -
117B GLU 3.7 1.3 - - - -
119B GLU* 1.3 76.8 - - - +
121B LEU* 1.3 62.4 + - - +
123B ARG* 3.1 6.6 + - - +
124B LEU* 3.0 31.3 + - - +
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Residues in contact with LEU 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B VAL* 3.7 21.3 - - + +
81B GLU* 4.0 7.9 - - - +
82B GLY* 4.2 19.3 - - - +
108B GLY* 4.6 4.3 - - - -
117B GLU 2.9 13.4 + - - +
118B VAL* 2.7 17.9 + - - +
120B GLY* 1.3 70.7 - - - +
122B LYS* 1.3 62.8 + - - +
124B LEU* 2.8 10.9 + - + +
125B MET* 2.8 39.3 + - + +
141B ILE* 3.7 23.1 - - + -
175B PHE* 3.4 40.4 - - + -
177B VAL* 4.7 1.3 - - + -
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Residues in contact with LYS 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B VAL* 2.9 35.8 + - + +
119B GLU* 3.5 13.9 - - + +
121B LEU* 1.3 70.8 - - - +
123B ARG* 1.3 55.3 + - - +
125B MET* 4.3 2.5 - - - -
126B THR* 2.7 39.6 + - - +
139B TRP* 3.1 52.8 + - + +
140B VAL* 5.5 0.2 - - - +
141B ILE* 4.0 10.1 - - + +
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Residues in contact with ARG 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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110B GLU 3.5 20.0 + - - -
111B LEU* 4.4 0.8 - - - +
112B ASN* 4.0 21.2 + - - +
115B GLU* 2.8 40.3 + - - +
119B GLU 3.1 13.3 + - - +
120B GLY* 3.1 20.5 + - - +
122B LYS* 1.3 77.9 - - - +
124B LEU* 1.3 79.9 + - - +
126B THR* 4.0 4.6 - - - -
127B GLU* 3.0 39.3 + - + +
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Residues in contact with LEU 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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80B VAL* 3.6 29.8 - - + -
108B GLY* 4.1 16.4 - - - +
109B GLY* 3.7 31.2 - - - +
110B GLU 3.9 4.9 - - - +
111B LEU* 4.2 2.0 - - + -
120B GLY 3.0 20.2 + - - +
121B LEU* 2.8 9.6 + - + +
123B ARG* 1.3 102.4 - - - +
125B MET* 1.3 59.3 + - - +
127B GLU* 3.0 17.4 + - - +
128B ILE* 2.8 40.0 + - - +
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Residues in contact with MET 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B GLY* 4.3 8.1 - - - -
84B LEU* 3.4 40.2 - - + -
107B PRO* 4.0 32.1 - - + +
121B LEU* 2.8 40.6 + - + +
122B LYS* 3.6 2.7 - - - +
124B LEU* 1.3 72.8 - - - +
126B THR* 1.3 56.3 + - - +
127B GLU 2.8 2.6 + - - -
128B ILE* 4.1 3.8 - - - -
129B LEU* 2.7 38.6 + - + +
139B TRP* 3.2 41.3 - - + +
141B ILE* 5.1 1.8 - - + -
177B VAL* 4.5 7.2 - - + -
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Residues in contact with THR 126 (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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50B LYS* 4.7 1.6 + - - -
122B LYS* 2.7 24.0 + - - +
123B ARG* 4.1 5.4 - - - -
125B MET* 1.3 74.2 - - - +
127B GLU* 1.3 55.5 + - - +
129B LEU 2.5 22.1 - - - +
130B GLY* 4.1 10.0 - - - -
131B ARG 5.9 0.2 - - - +
139B TRP* 2.7 22.8 + - - +
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Residues in contact with GLU 127 (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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50B LYS* 3.1 23.9 + - - +
53B LEU* 5.2 13.4 - - + +
123B ARG* 3.0 39.1 + - - +
124B LEU* 3.0 21.0 + - - +
125B MET 2.8 1.8 + - - -
126B THR* 1.3 77.1 - - - +
128B ILE* 1.3 61.7 + - + +
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Residues in contact with ILE 128 (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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50B LYS* 3.9 2.6 + - - -
53B LEU* 5.4 10.3 - - + -
97B LEU* 3.3 32.5 - - + -
105B LYS* 5.2 11.4 - - - +
107B PRO* 3.9 18.4 - - + -
108B GLY 4.8 5.8 - - - +
124B LEU 2.8 23.4 + - - +
125B MET* 3.4 4.9 - - - +
127B GLU* 1.3 77.8 - - + +
129B LEU* 1.3 86.6 + - + +
186B ALA 3.3 9.2 - - - +
188B PRO* 3.5 25.8 - - + +
191B TYR* 5.7 5.4 - - + -
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Residues in contact with LEU 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B LYS* 3.6 8.4 + - - -
84B LEU* 5.6 4.0 - - + -
97B LEU* 4.5 11.7 - - + -
107B PRO* 4.1 17.0 - - + -
125B MET* 2.7 22.9 + - + +
126B THR 2.5 26.7 - - - +
127B GLU 3.5 2.6 - - - +
128B ILE* 1.3 112.9 - - + +
130B GLY* 1.3 59.8 + - - +
139B TRP* 4.9 5.4 - - + -
185B PHE* 4.2 24.2 - - + -
186B ALA 3.3 26.2 - - - +
187B VAL* 4.1 15.7 - - + +
188B PRO* 4.4 0.2 - - + -
193B LEU* 5.2 3.8 - - + -
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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