Contacts of the helix formed by residues 112 - 125 (chain B) in PDB entry 2EIT
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 ARG 112 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B ARG* 5.7 1.6 - - - -
108B LEU* 3.3 16.9 + - - +
109B MET 3.0 8.0 + - - +
111B ARG* 1.3 82.7 - - + +
113B LYS* 1.3 62.9 + - - +
114B ARG 3.4 2.9 - - - -
115B GLU* 3.2 39.9 + - - +
116B LEU* 3.0 28.4 + - + +
218B LYS* 3.7 15.2 + - - +
221B GLU* 2.8 44.9 + - - +
222B ILE* 3.9 27.9 - - + +
225B GLU* 4.6 15.0 + - - -
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Residues in contact with LYS 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B GLU* 2.7 38.9 + - - +
10B PRO* 4.2 10.3 + - - +
12B GLU* 6.0 1.0 - - - +
109B MET 3.1 7.6 + - - +
110B ARG* 3.4 26.4 + - - +
111B ARG 3.5 1.4 - - - -
112B ARG* 1.3 76.7 - - - +
114B ARG* 1.3 96.0 + - + +
116B LEU* 3.2 2.3 + - - +
117B GLU* 2.9 38.6 + - - +
135B VAL* 4.0 22.2 - - + +
136B ALA* 6.3 0.4 - - - +
139B ILE* 4.6 3.6 - - + -
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Residues in contact with ARG 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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12B GLU* 3.4 37.8 + - - +
14B PHE* 4.0 7.8 - - - -
19B ALA* 5.5 3.4 + - - +
22B ALA* 4.1 21.2 - - + +
23B MET* 4.1 25.2 - - - +
26B ALA* 3.5 18.7 - - + +
112B ARG 3.4 1.0 - - - -
113B LYS* 1.3 106.3 - - + +
115B GLU* 1.3 58.5 + - - +
117B GLU* 2.7 44.6 + - - +
118B ALA* 2.8 30.7 + - - +
132B SER* 4.1 0.4 + - - -
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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
----------------------------------------------------------
26B ALA* 3.9 10.0 - - + +
29B ARG* 3.3 44.0 + - + +
30B VAL* 3.6 18.7 - - + +
33B GLU* 4.7 3.9 - - - +
36B ARG* 5.0 1.6 + - - -
112B ARG* 3.2 53.9 + - - +
114B ARG* 1.3 79.4 - - - +
116B LEU* 1.3 55.2 + - - +
118B ALA 3.4 0.7 + - - -
119B THR* 2.7 39.2 + - - +
218B LYS* 3.8 18.8 + - + +
221B GLU* 4.6 1.6 - - - +
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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
----------------------------------------------------------
109B MET* 3.7 36.3 - - + +
112B ARG* 3.0 25.2 + - + +
113B LYS 3.7 1.1 - - - +
115B GLU* 1.3 75.9 - - + +
117B GLU* 1.3 63.9 + - - +
119B THR* 3.2 5.5 + - - -
120B LEU* 2.9 26.2 + - - +
135B VAL* 3.7 24.7 - - + -
187B VAL* 4.6 7.6 - - + -
215B VAL* 4.3 13.1 - - + +
218B LYS* 3.9 33.4 - - + -
219B VAL* 4.7 5.4 - - + +
222B ILE* 3.8 21.5 - - + -
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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
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14B PHE* 3.5 11.9 - - - -
23B MET* 3.9 7.2 - - + +
113B LYS* 2.9 24.7 + - - +
114B ARG* 2.7 50.8 + - - +
116B LEU* 1.3 74.0 - - - +
118B ALA* 1.3 59.2 + - - +
120B LEU* 3.0 6.5 + - - +
121B VAL* 2.9 31.0 + - - +
131B ALA* 3.4 17.6 - - + +
132B SER* 3.0 40.2 + - - +
135B VAL* 3.8 11.1 - - + +
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Residues in contact with ALA 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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23B MET* 4.5 3.1 - - - +
26B ALA* 3.7 20.2 - - + +
27B LEU* 3.8 23.1 - - + +
30B VAL* 3.7 22.4 - - + -
114B ARG 2.8 18.0 + - - +
117B GLU* 1.3 78.4 - - - +
119B THR* 1.3 61.5 + - - +
121B VAL* 3.2 5.4 + - - +
122B TYR* 3.0 27.5 + - - -
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Residues in contact with THR 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B VAL* 3.6 10.8 - - + +
115B GLU 2.7 20.6 + - - -
116B LEU* 3.2 5.8 + - - -
118B ALA* 1.3 76.0 - - - +
120B LEU* 1.3 58.5 + - - +
122B TYR* 3.4 1.1 + - - +
123B GLU* 2.8 40.0 + - + +
214B VAL* 4.1 11.0 - - + -
215B VAL* 3.8 30.3 - - + +
218B LYS* 2.7 43.3 + - + +
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Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LEU 2.9 13.9 + - - +
117B GLU 3.3 6.7 - - - +
119B THR* 1.3 73.9 - - - +
121B VAL* 1.3 66.3 + - - +
123B GLU* 5.1 0.7 - - - -
124B VAL* 3.0 33.9 + - + +
125B GLY 3.3 5.4 + - - -
126B LYS* 3.6 6.9 + - + -
131B ALA* 3.6 22.4 - - + +
134B ASP* 3.5 35.7 - - + +
135B VAL* 3.8 15.0 - - + -
186B PRO* 3.5 37.2 - - + -
187B VAL* 3.8 15.5 - - + -
215B VAL* 4.1 7.4 - - + -
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Residues in contact with VAL 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B MET* 4.2 16.2 - - + -
27B LEU* 4.0 9.9 - - + -
57B ASN* 5.0 1.7 - - - +
59B SER* 5.1 0.3 + - - -
117B GLU 2.9 20.7 + - - +
118B ALA* 3.4 8.7 - - - +
120B LEU* 1.3 76.1 - - - +
122B TYR* 1.3 61.4 + - + +
125B GLY* 3.1 25.8 + - - -
126B LYS 3.3 22.2 - - - +
127B ASN 4.2 2.9 - - - +
128B TRP* 4.3 6.3 - - + -
131B ALA* 3.9 11.7 - - + -
354B ALA* 3.7 5.0 - - - +
355B GLU* 3.5 42.4 - - + +
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Residues in contact with TYR 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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27B LEU* 3.5 40.8 - - + +
30B VAL* 3.9 12.3 - - + -
31B ARG* 3.1 34.4 + - + -
34B PHE* 3.5 32.3 - + + -
57B ASN* 3.3 33.8 - - - +
58B PRO* 3.3 19.2 - - - +
59B SER* 6.4 0.2 - - - -
63B GLU* 5.3 0.9 - - - -
65B VAL* 3.8 3.9 - - + +
118B ALA 3.0 22.4 + - - +
119B THR 4.2 1.6 - - - +
121B VAL* 1.3 80.2 - - + +
123B GLU* 1.3 58.7 + - - +
355B GLU* 2.7 47.7 + - + -
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Residues in contact with GLU 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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55B SER* 2.5 29.9 + - - +
56B LEU 4.4 0.2 - - - -
58B PRO* 3.2 8.7 - - - +
65B VAL* 4.1 11.0 - - + -
119B THR* 2.8 26.5 + - + +
120B LEU* 5.1 0.9 - - - -
122B TYR* 1.3 74.5 - - - +
124B VAL* 1.3 61.5 + - + +
211B ASP 3.4 7.6 - - - +
212B ALA* 3.5 12.1 - - - -
213B VAL 3.3 6.1 + - - -
214B VAL* 2.9 28.1 + - + +
215B VAL* 2.8 38.7 + - + +
364B VAL* 4.6 0.5 - - - +
2521B NA 2.5 26.9 - - - -
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Residues in contact with VAL 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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58B PRO* 3.7 6.5 - - - +
120B LEU* 3.0 37.0 + - + +
123B GLU* 1.3 84.4 - - + +
125B GLY* 1.3 61.8 + - - +
126B LYS* 3.9 18.2 - - + -
183B TRP* 3.7 20.6 - - + +
186B PRO* 4.2 6.3 - - + -
211B ASP 3.8 16.4 - - - +
212B ALA* 3.9 13.2 - - + -
215B VAL* 5.7 0.4 - - + -
317B PHE* 3.2 21.6 - - + -
362B PRO 4.6 3.3 - - - +
364B VAL* 4.0 23.3 - - + +
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Residues in contact with GLY 125 (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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58B PRO* 3.7 13.8 - - - +
59B SER* 4.7 0.9 - - - -
120B LEU 3.3 0.2 + - - -
121B VAL 3.1 17.3 + - - -
124B VAL* 1.3 79.2 - - - +
126B LYS* 1.3 63.8 + - - +
127B ASN 3.7 1.2 + - - -
317B PHE* 3.8 1.1 - - - -
318B GLN* 3.1 22.5 + - - -
354B ALA* 3.6 14.1 - - - +
361B GLY* 3.9 5.4 - - - -
362B PRO* 4.0 9.6 - - - -
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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
------------------------------------------------------------
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