Contacts of the helix formed by residues 112 - 125 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ARG* 5.5 1.0 - - - +
108A LEU* 3.2 12.3 + - - +
109A MET 2.9 7.4 + - - +
111A ARG* 1.3 79.6 - - + +
113A LYS* 1.3 65.1 + - - +
114A ARG 3.4 2.2 - - - -
115A GLU* 2.7 51.2 + - - +
116A LEU* 3.0 25.9 + - + +
218A LYS* 3.7 18.9 + - - +
221A GLU* 2.8 46.9 + - - +
222A ILE* 3.8 25.4 - - + +
225A GLU* 5.6 7.1 + - - -
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Residues in contact with LYS 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLU* 2.7 33.6 + - + +
10A PRO* 4.2 10.5 + - - +
12A GLU* 5.9 1.4 - - - +
109A MET 3.1 8.8 + - - +
110A ARG* 3.3 24.3 + - - +
111A ARG 3.4 1.0 + - - -
112A ARG* 1.3 78.0 - - - +
114A ARG* 1.3 94.1 + - + +
116A LEU* 3.2 2.4 + - - +
117A GLU* 2.9 39.7 + - - +
132A SER* 5.6 0.6 + - - +
135A VAL* 3.9 20.9 - - + -
136A ALA* 6.5 0.9 - - + -
139A ILE* 4.6 5.8 - - + -
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Residues in contact with ARG 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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12A GLU* 3.4 38.4 + - - +
14A PHE* 3.9 5.9 - - - -
19A ALA* 4.8 4.0 - - - +
22A ALA* 4.1 21.2 - - + +
23A MET* 4.1 28.6 - - - +
26A ALA* 3.5 18.6 - - + +
112A ARG 3.4 0.6 - - - -
113A LYS* 1.3 106.7 - - + +
115A GLU* 1.3 58.5 + - - +
117A GLU* 2.7 43.5 + - - +
118A ALA* 2.8 31.7 + - - +
132A SER* 4.0 0.4 + - - -
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Residues in contact with GLU 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ALA* 4.0 10.2 - - + +
30A VAL* 3.7 9.8 - - + +
33A GLU* 4.6 4.9 - - - +
36A ARG* 5.2 1.0 + - - -
112A ARG* 2.7 57.6 + - - +
114A ARG* 1.3 77.2 - - - +
116A LEU* 1.3 60.2 + - - +
118A ALA* 3.3 4.2 + - - +
119A THR* 2.8 31.9 + - - -
218A LYS* 2.9 29.1 + - + +
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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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109A MET* 3.7 37.5 - - + +
112A ARG* 3.0 25.4 + - + +
113A LYS 3.7 3.6 - - - +
115A GLU* 1.3 74.4 - - + +
117A GLU* 1.3 67.1 + - - +
119A THR* 3.2 6.2 + - - -
120A LEU* 3.0 26.2 + - - +
135A VAL* 3.8 20.4 - - + -
187A VAL* 4.6 8.7 - - + -
215A VAL* 4.3 14.6 - - + +
218A LYS* 3.8 35.4 - - + -
219A VAL* 4.7 2.7 - - + +
222A ILE* 3.8 19.1 - - + -
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Residues in contact with GLU 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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14A PHE* 3.4 11.8 - - - -
23A MET* 3.9 7.9 - - + +
113A LYS* 2.9 26.8 + - - +
114A ARG* 2.7 51.7 + - - +
116A LEU* 1.3 75.7 - - - +
118A ALA* 1.3 61.9 + - - +
120A LEU* 3.1 6.5 + - - +
121A VAL* 3.0 25.9 + - - +
131A ALA* 3.4 14.9 - - + +
132A SER* 2.9 38.1 + - - +
135A VAL* 3.7 15.9 - - + +
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Residues in contact with ALA 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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23A MET* 4.2 2.4 - - - +
26A ALA* 3.6 32.1 - - + +
27A LEU* 3.7 23.6 - - + +
30A VAL* 3.6 8.1 - - + -
114A ARG 2.8 20.6 + - - +
115A GLU 3.6 4.7 - - - +
117A GLU* 1.3 72.7 - - - +
119A THR* 1.3 61.6 + - - +
121A VAL* 3.3 3.4 + - - +
122A TYR* 3.2 29.5 + - - -
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Residues in contact with THR 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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30A VAL* 3.7 13.7 - - + +
65A VAL* 5.2 3.8 - - + -
115A GLU 2.8 18.1 + - - -
116A LEU 3.6 6.1 - - - -
118A ALA* 1.3 77.5 - - - +
120A LEU* 1.3 56.9 + - - +
122A TYR* 3.5 1.1 + - - +
123A GLU* 2.8 33.1 + - + +
214A VAL* 4.2 14.1 - - + -
215A VAL* 3.8 29.8 - - + +
218A LYS* 3.0 36.0 + - + +
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Residues in contact with LEU 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 12.4 + - - +
117A GLU 3.1 6.7 + - - +
119A THR* 1.3 73.9 - - - +
121A VAL* 1.3 64.9 + - - +
123A GLU* 4.9 0.9 - - + -
124A VAL* 3.0 33.4 + - + +
125A GLY 3.2 5.9 + - - -
126A LYS* 3.6 6.1 + - + -
131A ALA* 3.7 22.0 - - + +
134A ASP* 3.6 35.0 - - + +
135A VAL* 3.7 16.2 - - + -
186A PRO* 3.5 37.2 - - + -
187A VAL* 3.9 14.8 - - + -
215A VAL* 4.2 7.4 - - + -
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Residues in contact with VAL 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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23A MET* 4.1 18.2 - - + -
27A LEU* 3.8 12.8 - - + -
57A ASN* 5.0 0.2 - - - +
59A SER* 5.0 1.6 + - - -
117A GLU 3.0 18.5 + - - +
118A ALA 3.3 7.6 + - - +
120A LEU* 1.3 75.1 - - - +
122A TYR* 1.3 61.3 + - + +
125A GLY* 3.2 24.6 + - - -
126A LYS 3.3 18.6 - - - +
127A ASN 4.1 3.4 - - - +
128A TRP* 4.3 6.1 - - + -
131A ALA* 3.9 11.9 - - + -
354A ALA* 3.5 11.5 - - - +
355A GLU* 3.5 37.5 - - + +
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Residues in contact with TYR 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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27A LEU* 3.4 48.1 + - + +
30A VAL* 3.7 15.9 - - + -
31A ARG* 3.9 20.6 - - + +
34A PHE* 3.6 32.1 - + + -
57A ASN* 3.3 27.3 - - - +
58A PRO* 3.2 20.6 - - - +
59A SER* 6.4 0.2 - - - -
63A GLU* 5.7 0.2 - - - -
65A VAL* 3.7 5.7 - - + +
118A ALA 3.2 21.1 + - - +
119A THR 4.2 1.8 - - - +
121A VAL* 1.3 81.9 - - + +
123A GLU* 1.3 57.7 + - - +
355A GLU* 2.9 46.7 + - + +
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Residues in contact with GLU 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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55A SER* 2.6 30.0 + - - +
58A PRO* 3.4 9.1 - - - +
65A VAL* 4.2 14.1 - - + -
119A THR* 2.8 22.5 + - + +
120A LEU* 4.9 1.3 - - - -
122A TYR* 1.3 74.9 - - - +
124A VAL* 1.3 62.0 + - + +
211A ASP 3.4 5.2 - - - +
212A ALA* 3.4 11.6 - - - +
213A VAL 3.2 6.4 + - - -
214A VAL* 2.9 28.9 + - - +
215A VAL* 2.8 37.6 + - + +
364A VAL* 4.8 1.2 - - - +
1521A NA 2.6 25.9 - - - -
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Residues in contact with VAL 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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58A PRO* 3.8 8.4 - - - +
120A LEU* 3.0 34.5 + - + +
123A GLU* 1.3 84.7 - - + +
125A GLY* 1.3 63.3 + - - +
126A LYS* 3.9 19.5 - - + -
183A TRP 3.7 20.4 - - - +
186A PRO* 4.2 6.1 - - + -
211A ASP 3.8 15.7 - - - +
212A ALA* 3.9 12.8 - - + -
317A PHE* 3.2 22.6 - - + -
362A PRO 4.7 3.1 - - - +
364A VAL* 4.0 21.9 - - + +
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Residues in contact with GLY 125 (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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58A PRO* 3.6 16.2 - - - +
59A SER* 4.7 0.4 - - - -
120A LEU 3.2 0.4 + - - -
121A VAL 3.2 18.1 + - - -
124A VAL* 1.3 78.6 - - - +
126A LYS* 1.3 63.0 + - - +
127A ASN 3.8 1.2 + - - -
317A PHE* 3.8 1.1 - - - -
318A GLN* 3.1 22.2 + - - -
354A ALA* 3.6 14.7 - - - +
361A GLY* 3.9 2.1 - - - -
362A PRO* 3.8 11.1 - - - +
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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