Contacts of the helix formed by residues 93 - 112 (chain A) in PDB entry 3EBV
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 SER 93 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A PRO* 5.7 0.5 - - - +
92A ASN* 1.3 83.0 + - - +
94A SER* 1.3 59.3 + - - +
95A ALA* 3.6 6.6 + - - +
96A SER* 2.7 31.5 + - - -
97A ALA* 2.9 29.1 + - - +
128A TYR* 3.3 19.2 - - - +
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Residues in contact with SER 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A SER* 1.3 73.7 - - - +
95A ALA* 1.3 65.0 + - - +
97A ALA* 3.3 2.9 + - - +
98A THR* 2.9 27.8 + - - -
128A TYR* 3.7 7.4 - - - -
131A GLN* 3.0 30.8 + - - +
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Residues in contact with ALA 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A PRO* 6.4 0.9 - - + -
93A SER* 3.3 7.2 + - - +
94A SER* 1.3 79.1 - - - +
96A SER* 1.3 57.1 + - - +
98A THR* 3.3 6.1 + - - -
99A ASN* 2.8 41.9 + - - +
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Residues in contact with SER 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A PRO* 3.5 32.0 - - - +
45A GLY* 3.6 4.0 - - - -
90A SER 3.7 17.3 - - - -
91A VAL* 3.6 2.4 - - - -
92A ASN* 2.9 29.1 + - - -
93A SER* 2.7 26.4 + - - -
95A ALA* 1.3 73.1 - - - +
97A ALA* 1.3 59.8 + - - +
100A PHE* 2.8 31.2 + - - +
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Residues in contact with ALA 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A VAL* 3.8 5.1 - - + +
93A SER 2.9 19.3 + - - +
94A SER 3.5 4.5 - - - +
96A SER* 1.3 77.8 + - - +
98A THR* 1.3 56.5 + - - +
100A PHE* 3.4 3.3 + - - +
101A ALA* 3.0 26.7 + - - +
128A TYR* 3.5 24.5 - - + +
131A GLN* 4.1 15.5 - - + -
132A ALA* 3.5 25.7 - - + +
135A ALA* 5.6 0.9 - - - -
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Residues in contact with THR 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A SER* 2.9 19.5 + - - -
95A ALA* 3.6 7.0 - - - +
97A ALA* 1.3 71.4 - - - +
99A ASN* 1.3 64.5 + - - +
101A ALA* 3.4 4.6 + - - +
102A ASN* 2.9 49.0 + - - +
131A GLN* 4.5 7.3 + - - -
135A ALA* 5.5 4.0 - - - -
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Residues in contact with ASN 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A THR* 3.3 21.8 - - - +
44A PRO* 2.9 33.1 + - - +
45A GLY 4.0 1.6 - - - -
46A ALA* 4.0 10.4 - - + +
95A ALA* 2.8 27.7 + - - +
96A SER* 3.8 0.6 - - - +
98A THR* 1.3 77.1 - - - +
100A PHE* 1.3 63.9 + - - +
102A ASN* 4.0 7.6 + - - +
103A SER* 2.7 32.0 + - - -
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Residues in contact with PHE 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A GLY 3.1 21.9 + - - +
47A VAL* 4.6 2.2 - - + -
82A VAL* 4.0 27.1 - - + -
89A VAL* 4.3 5.4 - - + -
91A VAL* 3.7 22.7 - - + -
96A SER 2.8 18.7 + - - +
97A ALA 3.5 4.5 - - - +
98A THR 3.2 0.2 - - - -
99A ASN* 1.3 77.4 - - - +
101A ALA* 1.3 60.8 + - - +
103A SER* 3.8 1.3 - - - -
104A VAL* 2.9 59.2 + - + +
116A VAL* 4.7 0.9 - - + -
118A ILE* 3.7 27.1 - - + -
120A LEU* 5.4 1.1 - - + -
129A MSE 4.0 18.6 - - + -
132A ALA* 3.9 17.3 - - + -
133A LEU* 4.4 9.9 - - + -
136A LEU* 4.6 6.5 - - + -
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Residues in contact with ALA 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ALA 3.0 11.5 + - - +
98A THR* 3.9 3.8 - - - +
100A PHE* 1.3 79.1 - - - +
102A ASN* 1.3 64.0 + - - +
105A TYR* 3.1 26.7 + - - +
132A ALA 3.6 6.1 - - - +
135A ALA* 3.6 18.4 - - + -
136A LEU* 3.5 41.0 - - - +
139A LYS* 4.0 7.9 - - - +
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Residues in contact with ASN 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A THR* 2.9 39.8 + - - +
99A ASN* 4.0 8.4 + - - +
101A ALA* 1.3 78.3 - - - +
103A SER* 1.3 57.6 + - - +
105A TYR* 3.9 2.6 - - - +
106A SER* 3.0 27.4 + - - -
139A LYS* 2.9 32.9 + - - +
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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
----------------------------------------------------------
46A ALA* 3.4 8.4 - - - -
47A VAL* 2.9 44.1 + - - +
99A ASN 2.7 22.7 + - - -
100A PHE* 3.3 4.0 + - - -
102A ASN* 1.3 74.7 - - - +
104A VAL* 1.3 68.5 + - - +
106A SER* 3.3 6.3 + - - -
107A VAL* 3.0 27.5 + - - +
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Residues in contact with VAL 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A VAL* 3.7 22.2 - - + -
80A ILE* 4.5 6.1 - - + -
82A VAL* 4.4 6.3 - - + -
100A PHE* 2.9 47.7 + - + +
101A ALA 4.3 0.4 - - - +
103A SER* 1.3 76.0 + - - +
105A TYR* 1.3 57.3 + - - +
107A VAL* 3.2 4.0 + - - +
108A MSE 2.9 38.4 + - + +
116A VAL* 3.9 19.5 - - + -
136A LEU* 3.6 27.8 - - + -
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Residues in contact with TYR 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ALA 3.1 19.1 + - - +
102A ASN 3.9 2.9 - - - +
104A VAL* 1.3 77.7 - - - +
106A SER* 1.3 58.8 + - - +
108A MSE 3.2 12.6 + - + +
109A ARG* 2.9 68.0 + - + +
136A LEU* 3.7 10.9 - - + +
139A LYS* 3.4 53.9 + - + -
140A ALA* 3.7 21.3 - - + -
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Residues in contact with SER 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ASN 3.0 18.3 + - - -
103A SER* 3.3 8.5 + - - -
105A TYR* 1.3 79.1 - - - +
107A VAL* 1.3 58.6 + - - +
109A ARG* 3.4 5.1 + - - +
110A GLU* 2.9 30.0 + - - +
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Residues in contact with VAL 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A VAL* 4.3 8.5 - - + +
48A THR* 4.1 12.1 - - - +
49A PHE* 3.9 35.9 - - + +
80A ILE* 4.2 14.4 - - + -
103A SER 3.0 18.3 + - - +
104A VAL* 3.2 8.7 + - - +
106A SER* 1.3 75.1 - - - +
108A MSE 1.3 66.0 + - - +
110A GLU* 3.4 1.9 + - - -
111A TYR* 3.1 33.8 + - + +
113A PHE* 3.7 24.4 - - + -
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Residues in contact with MSE 108 (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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80A ILE* 4.4 4.0 - - + -
104A VAL* 2.9 37.4 + - + +
105A TYR* 3.5 13.2 - - + +
107A VAL* 1.3 77.0 - - - +
109A ARG* 1.3 58.7 + - + +
112A GLY* 2.8 29.5 + - - -
113A PHE* 3.0 30.4 + - + +
114A ASP 3.9 3.8 - - - +
115A GLY* 3.7 46.0 - - - +
136A LEU* 4.2 15.0 - - - -
140A ALA* 3.9 24.5 - - + -
144A MSE 4.0 7.9 - - + +
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Residues in contact with ARG 109 (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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105A TYR* 2.9 61.2 + - + +
106A SER* 3.9 5.2 - - - +
108A MSE 1.3 78.0 - - - +
110A GLU* 1.3 64.0 + - - +
111A TYR 3.5 0.3 + - - -
112A GLY* 3.8 6.0 + - - -
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Residues in contact with GLU 110 (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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61A VAL* 5.5 0.7 - - - +
65A LYS* 2.9 39.9 + - - +
106A SER* 2.9 19.1 + - - +
107A VAL* 4.5 1.1 - - - -
108A MSE 3.3 0.2 - - - -
109A ARG* 1.3 78.8 - - - +
111A TYR* 1.3 92.5 + - + +
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Residues in contact with TYR 111 (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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49A PHE* 3.3 46.2 + + + -
50A ASN* 5.1 1.4 - - - -
51A LEU* 5.1 1.4 + - + -
61A VAL* 4.1 21.3 - - + +
64A PHE* 3.9 22.0 - + + -
65A LYS* 3.9 35.6 - - + +
68A VAL* 4.0 18.0 - - - +
69A ARG* 6.0 0.9 - - - +
107A VAL* 3.1 23.4 + - + +
110A GLU* 1.3 96.4 + - + +
112A GLY* 1.3 62.0 + - - +
113A PHE* 3.6 34.2 - + + -
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Residues in contact with GLY 112 (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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68A VAL* 4.6 1.8 - - - -
72A GLN* 2.8 29.5 + - - +
108A MSE 2.8 11.1 + - - -
109A ARG* 3.8 5.1 + - - -
110A GLU 3.6 2.0 - - - -
111A TYR* 1.3 79.1 - - - +
113A PHE* 1.3 61.9 + - - -
114A ASP* 4.6 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