Contacts of the helix formed by residues 84 - 103 (chain A) in PDB entry 2E9A
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 ALA 84 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A VAL 3.2 4.1 - - - +
83A SER* 1.3 78.2 - - - +
85A LEU* 1.3 58.9 + - + +
87A GLU* 2.6 48.9 + - - +
88A LEU* 3.0 10.5 + - + +
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Residues in contact with LEU 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A SER* 5.6 2.0 - - - +
82A VAL* 3.6 26.8 + - + +
84A ALA* 1.3 80.0 - - + +
86A MET* 1.3 58.0 + - - +
87A GLU 2.8 6.4 + - - -
88A LEU* 3.1 18.6 + - + +
89A PHE* 3.0 25.9 + - - +
702A B28 3.8 53.2 - - + +
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Residues in contact with MET 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A TYR* 6.2 3.6 - - + -
69A ALA 5.3 2.0 - - - +
82A VAL* 3.2 19.0 + - + +
83A SER* 4.0 6.3 - - - +
84A ALA 3.2 0.8 - - - -
85A LEU* 1.3 76.2 - - - +
87A GLU* 1.3 56.4 + - - +
89A PHE* 4.2 17.3 - - + -
90A VAL* 3.1 26.0 - - - +
116A PHE* 3.3 26.3 - - + -
142A ALA 4.9 2.9 - - - +
143A ALA* 3.7 14.4 - - - -
144A ASN* 3.3 42.0 - - + +
145A TYR 5.0 0.9 - - - +
702A B28 3.6 38.4 - - + -
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Residues in contact with GLU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A SER* 3.3 15.2 - - - +
84A ALA* 2.6 37.9 + - - +
86A MET* 1.3 72.5 - - - +
88A LEU* 1.3 52.9 + - + +
90A VAL* 3.0 3.4 + - - -
91A TRP* 2.6 66.2 + - + +
116A PHE* 5.0 9.9 - - + -
117A ASN* 5.6 3.1 + - - -
120A LEU* 5.9 2.0 - - + -
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Residues in contact with LEU 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ALA* 3.0 8.7 + - + +
85A LEU* 3.5 24.7 - - + +
87A GLU* 1.3 77.5 - - + +
89A PHE* 1.3 53.7 + - - +
91A TRP* 2.7 13.3 + - + +
92A ALA* 2.7 36.4 + - - +
702A B28 4.0 50.5 - - + +
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Residues in contact with PHE 89 (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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25A MET* 5.2 4.3 - - + -
69A ALA* 3.9 20.9 - - + -
85A LEU 3.0 13.7 + - - +
86A MET* 4.2 18.6 - - + -
88A LEU* 1.3 82.0 - - - +
90A VAL* 1.3 72.5 + - + +
92A ALA* 3.4 7.6 + - - +
93A LEU* 3.4 19.1 + - + +
141A ILE* 4.1 17.3 - - + -
142A ALA 3.7 21.3 - - - -
701A B28 3.7 35.6 - + - -
702A B28 3.3 45.4 - + + -
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Residues in contact with VAL 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A MET 3.1 21.1 - - - +
87A GLU 3.0 3.3 + - - +
89A PHE* 1.3 82.9 - - + +
91A TRP* 1.3 65.5 + - - +
93A LEU* 3.5 20.3 - - + +
94A ASP* 3.8 6.1 + - - +
109A ILE* 4.7 17.0 - - + -
116A PHE* 4.0 8.5 - - + -
120A LEU* 4.3 18.2 - - + +
124A ILE* 4.5 20.0 - - + -
141A ILE* 6.1 0.2 - - + -
143A ALA* 3.6 29.4 - - + -
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Residues in contact with TRP 91 (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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87A GLU* 2.6 58.8 + - + +
88A LEU* 2.7 11.5 + - + +
90A VAL* 1.3 70.0 - - - +
92A ALA* 1.3 65.2 + - - +
94A ASP* 2.8 23.9 + - - +
95A SER 4.4 0.2 + - - -
117A ASN* 4.5 5.8 - - - -
119A ARG* 5.6 4.5 - - - -
120A LEU* 2.9 32.5 - - + +
123A ARG* 2.9 44.8 + - - +
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Residues in contact with ALA 92 (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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88A LEU 2.7 15.6 + - - +
89A PHE* 3.6 11.2 - - - +
91A TRP* 1.3 72.9 - - - +
93A LEU* 1.3 54.5 + - - +
94A ASP 2.7 12.0 + - - -
95A SER* 3.2 15.8 + - - -
96A GLU* 4.0 5.7 + - - +
701A B28 4.0 28.6 - - + -
702A B28 5.4 8.3 - - + -
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Residues in contact with LEU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A VAL* 6.3 2.9 - - + -
89A PHE* 3.4 11.2 + - + +
90A VAL* 3.5 19.1 - - + +
91A TRP 3.2 0.2 - - - -
92A ALA* 1.3 76.8 - - - +
94A ASP* 1.3 60.6 + - - +
95A SER 3.5 0.2 - - - -
96A GLU* 3.3 22.5 - - + +
97A VAL* 3.2 20.8 + - + +
100A LEU* 5.0 5.8 - - + -
107A LEU* 4.9 12.3 - - + -
109A ILE* 3.8 22.9 - - + -
139A LEU* 6.0 0.2 - - + -
141A ILE* 3.2 43.1 - - + -
701A B28 4.9 13.4 - - + -
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Residues in contact with ASP 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A VAL 3.8 4.0 + - - +
91A TRP* 2.8 18.0 + - - +
92A ALA 2.7 7.3 + - - -
93A LEU* 1.3 71.2 - - - +
95A SER* 1.3 65.6 + - - +
96A GLU 3.0 1.3 - - - -
97A VAL* 3.0 28.6 + - - +
98A LYS* 4.4 5.7 + - - +
123A ARG* 3.8 38.0 + - - +
127A SER* 4.3 6.4 + - - -
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Residues in contact with SER 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A TRP 4.4 0.2 + - - -
92A ALA 3.2 9.0 + - - -
94A ASP* 1.3 79.5 - - - +
96A GLU* 1.3 65.5 + - - +
97A VAL 3.3 0.9 + - - -
98A LYS* 3.6 18.1 + - - +
99A SER* 4.2 3.8 + - - -
102A ARG* 5.6 0.2 + - - -
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Residues in contact with GLU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ARG* 2.8 45.9 + - - +
92A ALA 4.3 2.7 - - - +
93A LEU* 3.3 28.3 - - + +
94A ASP 3.0 0.4 - - - -
95A SER* 1.3 80.8 - - - +
97A VAL* 1.3 63.8 + - - +
99A SER* 3.3 17.4 + - - -
100A LEU* 2.9 33.1 + - + +
701A B28 3.9 29.3 - - + -
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Residues in contact with VAL 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A LEU* 3.2 15.6 + - + +
94A ASP* 3.0 19.5 + - - +
96A GLU* 1.3 76.8 - - - +
98A LYS* 1.3 62.8 + - + +
100A LEU* 3.2 8.4 + - + +
101A HIS* 2.8 27.5 + - - +
107A LEU* 3.9 20.6 - - + -
127A SER* 3.4 32.5 - - - +
130A LEU* 4.0 24.5 - - + -
131A THR* 4.8 5.9 - - + +
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Residues in contact with LYS 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 ASP 4.8 3.8 - - - +
95A SER* 3.6 11.4 + - - +
96A GLU 3.3 0.6 - - - -
97A VAL* 1.3 78.9 - - + +
99A SER* 1.3 68.5 + - - +
101A HIS* 3.2 7.5 + - - +
102A ARG* 2.9 47.7 + - - +
130A LEU* 5.8 4.3 - - + -
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Residues in contact with SER 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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95A SER 4.2 2.3 + - - -
96A GLU* 3.3 24.1 + - - -
98A LYS* 1.3 78.5 - - - +
100A LEU* 1.3 65.0 + - - +
102A ARG* 3.2 24.1 + - - +
103A HIS* 2.8 44.3 + - - -
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Residues in contact with LEU 100 (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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54A VAL* 4.3 11.2 - - + -
93A LEU* 5.0 7.6 - - + -
96A GLU* 2.9 33.3 + - + +
97A VAL* 3.6 7.0 - - - +
99A SER* 1.3 78.1 - - - +
101A HIS* 1.3 61.8 + - - +
103A HIS* 2.9 16.7 + - + +
105A VAL* 3.2 45.8 + - + +
107A LEU* 4.3 25.6 - - + -
131A THR* 5.3 3.4 - - + -
139A LEU* 3.8 32.1 - - + -
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Residues in contact with HIS 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 VAL 2.8 14.6 + - - +
98A LYS* 3.5 9.9 - - - +
100A LEU* 1.3 74.7 - - - +
102A ARG* 1.3 64.2 + - + +
104A ASN* 2.8 21.8 + - - -
130A LEU* 3.8 42.7 + - + +
131A THR* 3.9 13.5 - - + +
134A ASN* 3.0 38.0 + - - +
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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
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95A SER 5.6 0.2 + - - -
98A LYS* 2.9 39.6 + - - +
99A SER* 3.6 28.0 + - - +
101A HIS* 1.3 83.5 - - + +
103A HIS* 1.3 68.4 + - + +
104A ASN* 3.2 2.6 + - - +
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Residues in contact with HIS 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A SER* 6.4 2.2 - - - -
58A ALA* 5.8 3.6 - - - +
99A SER* 2.8 36.8 + - - +
100A LEU* 2.9 13.6 + - + +
102A ARG* 1.3 84.5 - - + +
104A ASN* 1.3 71.9 + - - +
105A VAL* 3.2 15.9 + - + +
136A GLY* 5.4 0.7 - - - -
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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