Contacts of the helix formed by residues 92 - 107 (chain A) in PDB entry 1EKV
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 92 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A PHE* 1.3 85.0 - - + +
93A PRO* 1.3 69.9 - - - +
94A TRP* 3.0 15.5 + - + -
95A LEU* 3.2 42.4 + - + +
96A ASN* 3.7 8.0 + - - -
269A VAL* 4.2 7.8 - - + +
272A GLN* 4.2 3.0 - - - +
273A SER* 2.8 40.5 + - - +
276A ASP* 2.7 29.1 + - - -
361A TRP* 2.9 70.6 + - + +
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Residues in contact with PRO 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A MET* 4.3 7.6 - - - -
90A LEU* 3.1 38.1 - - + +
91A PHE 3.1 2.8 - - - +
92A ARG* 1.3 90.2 - - - +
94A TRP* 1.3 72.5 + - + +
95A LEU 3.4 0.2 - - - -
96A ASN* 3.2 14.4 + - - +
97A MET* 3.1 25.7 + - - +
118A LEU* 3.5 26.9 - - + -
363A PHE* 3.4 25.8 - - + -
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Residues in contact with TRP 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ARG* 3.0 23.5 + - + -
93A PRO* 1.3 78.0 - - + +
95A LEU* 1.3 69.8 + - + +
97A MET* 3.0 10.0 + - - +
98A ASP* 2.9 30.9 + - - +
115A LEU* 5.3 11.9 - - + -
118A LEU* 3.5 24.2 - - + +
360A GLU 3.5 23.3 - - - -
361A TRP* 3.4 28.7 - + - -
362A MET 4.3 1.8 - - - -
363A PHE* 3.7 32.4 - + + -
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Residues in contact with LEU 95 (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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92A ARG* 3.2 54.5 + - + +
94A TRP* 1.3 80.2 - - + +
96A ASN* 1.3 57.0 + - - +
98A ASP* 3.4 18.4 - - + +
99A ARG* 3.1 27.2 + - - +
269A VAL* 3.9 29.7 - - + +
272A GLN* 4.2 20.0 - - + +
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Residues in contact with ASN 96 (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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76A GLU* 2.8 30.4 - - + +
77A GLY 3.4 12.2 + - - +
78A MET* 3.5 38.8 - - + +
91A PHE 4.1 7.3 + - - -
92A ARG 3.7 14.1 + - - -
93A PRO* 3.2 8.0 + - - +
94A TRP 3.1 0.4 - - - -
95A LEU* 1.3 76.4 - - - +
97A MET* 1.3 65.6 + - + +
99A ARG* 3.3 11.9 + - - +
100A MET* 2.8 30.8 + - - +
269A VAL* 3.7 16.2 - - - +
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Residues in contact with MET 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLU* 5.6 0.7 - - + -
78A MET* 3.8 28.9 - - + -
93A PRO 3.1 15.7 + - - +
94A TRP* 3.0 11.5 + - + +
96A ASN* 1.3 79.6 - - + +
98A ASP* 1.3 63.4 + - - +
100A MET* 3.2 13.2 + - - +
101A LEU* 2.9 24.9 + - - +
112A PHE* 4.9 2.9 - - - -
114A LYS* 3.5 44.7 - - + +
117A LEU* 3.6 32.3 - - + -
118A LEU* 4.0 15.9 - - + -
121A ILE* 3.9 9.6 - - + -
144A PRO* 4.9 2.0 - - + -
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Residues in contact with ASP 98 (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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94A TRP* 2.9 19.8 + - - +
95A LEU* 3.4 25.9 - - + +
97A MET* 1.3 75.1 - - - +
99A ARG* 1.3 63.5 + - - +
101A LEU* 3.1 5.2 + - - +
102A ARG* 2.9 30.1 + - + +
114A LYS* 3.1 36.2 + - - +
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Residues in contact with ARG 99 (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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76A GLU* 2.6 39.1 + - - +
77A GLY 4.3 4.8 + - - -
95A LEU 3.1 12.4 + - - +
96A ASN* 3.4 11.7 + - - +
98A ASP* 1.3 76.6 - - - +
100A MET* 1.3 67.3 + - - +
102A ARG* 3.1 24.2 + - - +
103A SER* 2.9 30.4 + - - +
200A ASN 5.3 0.4 - - - +
201A TYR* 5.7 0.2 - - - -
202A LYS* 3.6 21.0 - - + +
266A LEU* 3.2 31.8 - - + +
267A PRO* 3.1 31.8 + - + -
268A GLY* 3.5 3.0 - - - -
269A VAL* 3.7 6.5 - - - +
370A PLP 3.3 30.6 + - - -
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Residues in contact with MET 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LEU* 4.1 18.0 - - + +
75A PHE 5.6 0.2 - - - -
76A GLU* 3.7 17.8 + - + -
96A ASN 2.8 17.4 + - - +
97A MET* 3.5 10.1 - - - +
99A ARG* 1.3 75.1 - - - +
101A LEU* 1.3 66.2 + - - +
103A SER* 3.1 9.0 + - - -
104A ALA* 2.8 23.2 + - + +
112A PHE* 4.0 10.8 - - + -
117A LEU* 3.7 22.7 - - + -
144A PRO* 4.0 24.9 - - + -
145A VAL 4.3 4.3 - - - +
146A LEU* 4.1 17.0 - - + -
163A LEU* 3.9 34.5 - - + -
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Residues in contact with LEU 101 (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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97A MET 2.9 11.5 + - - +
98A ASP* 3.3 10.5 - - - +
100A MET* 1.3 78.6 - - - +
102A ARG* 1.3 62.5 + - + +
104A ALA* 3.2 7.0 + - + +
105A MET* 3.1 31.6 + - + +
111A SER* 4.0 15.3 - - - -
112A PHE* 3.7 57.8 - - + +
114A LYS* 3.7 37.0 - - + +
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Residues in contact with ARG 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ASP* 2.9 19.6 + - + +
99A ARG* 3.1 22.3 + - - +
101A LEU* 1.3 77.1 - - + +
103A SER* 1.3 61.7 - - - +
105A MET* 3.2 9.9 + - - +
106A ARG 3.2 16.3 + - - -
200A ASN* 2.9 35.7 + - - +
201A TYR* 3.5 34.8 + - + +
267A PRO* 3.4 25.9 - - - +
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Residues in contact with SER 103 (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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74A LEU* 4.0 15.9 - - - -
75A PHE 5.5 1.0 + - - -
76A GLU* 5.1 0.2 + - - -
99A ARG* 2.9 17.0 + - - +
100A MET* 3.4 9.3 - - - -
102A ARG* 1.3 72.5 - - - +
104A ALA* 1.3 66.9 + - - +
106A ARG* 3.0 13.5 + - - +
107A LEU* 3.3 16.3 + - - +
201A TYR* 3.7 14.2 - - - +
202A LYS* 3.5 22.6 + - - +
203A LEU* 3.7 20.4 - - - +
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Residues in contact with ALA 104 (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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74A LEU* 4.3 9.6 - - + +
100A MET 2.8 13.7 + - - +
101A LEU* 3.2 20.9 - - + +
103A SER* 1.3 78.8 - - - +
105A MET* 1.3 60.8 + - - +
107A LEU 3.6 0.5 + - - -
108A CYS 3.5 1.7 + - - -
109A LEU* 2.8 39.1 + - + +
110A PRO 4.3 11.2 - - - +
112A PHE* 4.8 2.0 - - + -
146A LEU* 4.1 21.8 - - + -
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Residues in contact with MET 105 (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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101A LEU* 3.1 21.7 + - + +
102A ARG* 3.6 9.2 - - - +
103A SER 3.1 0.4 - - - -
104A ALA* 1.3 75.7 - - - +
106A ARG* 1.3 66.0 + - - +
107A LEU 3.1 2.0 - - - -
108A CYS* 3.2 14.1 + - - +
109A LEU 4.3 9.6 - - - +
111A SER* 4.0 28.5 - - - +
212B LEU* 4.2 12.8 - - - +
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Residues in contact with ARG 106 (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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102A ARG 3.2 11.2 + - - +
103A SER 3.0 11.0 + - - +
105A MET* 1.3 78.1 - - - +
107A LEU* 1.3 62.8 + - + +
108A CYS 3.4 0.4 - - - -
196A GLY 5.2 0.6 + - - -
197A GLY 3.8 11.9 + - - -
198A VAL* 3.5 30.3 - - + +
201A TYR* 3.6 36.6 - - + -
203A LEU* 5.3 0.4 - - + -
190B PHE* 4.0 27.5 - - - -
209B PRO* 2.5 44.5 + - - +
212B LEU* 3.2 37.0 + - - +
213B VAL* 4.4 1.0 - - - +
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Residues in contact with LEU 107 (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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71A SER 4.1 5.8 - - - +
72A LEU* 3.9 22.3 - - + +
73A GLN 3.5 39.7 - - - +
74A LEU* 4.5 6.7 - - + -
103A SER 3.3 11.4 + - - +
104A ALA 3.6 0.4 + - - +
105A MET 3.1 0.4 - - - -
106A ARG* 1.3 83.9 - - + +
108A CYS* 1.3 71.4 + - - +
109A LEU* 3.1 14.0 + - + +
158A PRO* 4.5 3.3 - - - +
203A LEU* 3.9 32.1 - - + -
208B GLY* 3.7 32.3 - - - +
209B PRO* 3.9 6.7 - - + -
211B VAL* 4.8 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
------------------------------------------------------------
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