Contacts of the helix formed by residues 101 - 112 (chain A) in PDB entry 2Z98
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 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A SER* 2.8 36.8 + - - -
93A ALA* 6.1 0.2 - - - +
94A PRO* 3.7 8.7 + - - -
96A TYR* 3.6 29.2 - - - -
100A ILE* 1.3 78.8 - - - +
102A THR* 1.4 64.1 + - - +
103A GLN* 3.5 9.6 + - - -
104A LEU* 3.3 13.9 + - - +
105A LYS* 3.1 19.8 + - - +
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Residues in contact with THR 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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49A VAL* 5.1 7.6 - - + -
96A TYR* 5.3 0.6 - - - -
100A ILE 3.7 2.3 + - - -
101A SER* 1.4 57.5 - - - +
103A GLN* 1.4 67.9 + - - +
105A LYS* 4.0 14.4 - - + +
106A ASN* 2.9 50.3 + - - +
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Residues in contact with GLN 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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8A SER 3.8 14.1 - - - +
10A ILE* 3.2 30.9 - - - +
42A LEU* 3.6 42.6 - - + +
43A ALA* 4.0 14.8 - - + -
46A PRO* 5.8 3.8 - - + -
47A ILE* 4.8 3.6 + - - +
96A TYR* 4.9 0.5 - - - -
101A SER* 3.1 13.2 - - - -
102A THR* 1.4 86.9 + - - +
104A LEU* 1.3 61.4 + - - +
106A ASN* 3.8 8.2 + - - +
107A TYR* 3.7 11.3 + - - +
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Residues in contact with LEU 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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6A LEU* 5.0 4.7 - - + -
8A SER* 3.6 16.9 - - - +
42A LEU* 3.9 20.9 - - + -
91A ILE* 3.8 31.0 - - + -
92A ALA 4.1 4.7 - - - +
93A ALA* 4.1 18.8 - - + -
100A ILE* 3.8 23.8 - - + -
101A SER* 3.3 11.6 + - - +
103A GLN* 1.3 77.6 - - - +
105A LYS* 1.4 65.5 + - - +
107A TYR* 3.1 11.4 + - + +
108A PHE* 3.1 45.9 + - + -
156A LEU* 4.4 1.3 - - + -
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Residues in contact with LYS 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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99A ASN* 5.2 14.6 - - - +
100A ILE* 3.6 18.1 - - + +
101A SER 3.1 15.6 + - - +
102A THR* 3.2 17.2 + - + +
104A LEU* 1.4 75.8 - - - +
106A ASN* 1.3 66.3 - - - +
108A PHE* 3.2 6.9 + - + +
109A ASP* 2.9 44.5 + - - +
155A TYR* 4.5 12.6 - - - +
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Residues in contact with ASN 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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47A ILE* 3.0 38.4 + - + +
48A PRO 3.5 22.3 - - - +
49A VAL* 3.7 24.6 - - - +
50A LEU 4.5 2.5 + - - +
102A THR* 2.9 35.2 + - - +
103A GLN* 4.1 5.9 - - - +
105A LYS* 1.3 80.3 - - - +
107A TYR* 1.3 63.0 + - - +
109A ASP* 3.4 11.3 + - - +
110A LEU* 3.2 18.4 + - - +
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Residues in contact with TYR 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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4A LEU* 4.2 4.5 - - - +
6A LEU* 3.6 41.5 - - + +
40A ARG* 4.7 1.3 - - - -
42A LEU* 3.8 34.8 - - + -
47A ILE* 4.0 9.7 - - + +
79A LEU* 4.0 33.1 + - + -
82A GLU* 5.0 2.0 + - - -
83A LEU* 3.9 31.1 - - + +
91A ILE* 6.2 0.2 - - + -
103A GLN 3.7 3.5 + - - +
104A LEU* 3.1 12.3 + - + +
106A ASN* 1.3 76.0 - - - +
108A PHE* 1.3 90.4 + + - +
110A LEU* 3.1 4.3 + - - +
111A VAL* 3.0 46.9 + - + +
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Residues in contact with PHE 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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91A ILE* 4.6 8.1 - - + -
100A ILE* 3.8 18.8 - - + -
104A LEU* 3.1 30.4 + - + -
105A LYS* 3.2 7.2 + - + +
107A TYR* 1.3 95.6 - + - +
109A ASP* 1.4 61.2 + - - +
111A VAL* 3.8 2.4 - - + +
112A ALA* 3.1 33.3 + - - +
155A TYR* 3.6 22.2 - + - +
156A LEU* 3.6 33.4 - - + -
159A PHE* 3.4 46.7 - + + -
160A LEU* 4.5 14.1 - - + -
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Residues in contact with ASP 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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50A LEU* 3.9 41.2 + - + +
58A LEU* 4.2 8.5 - - - +
105A LYS* 2.9 45.9 + - - +
106A ASN* 3.8 11.4 - - - +
107A TYR 3.2 0.6 - - - -
108A PHE* 1.4 78.0 - - - +
110A LEU* 1.3 64.7 + - + +
112A ALA* 4.2 12.5 - - - +
159A PHE* 5.9 1.0 - - - -
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Residues in contact with LEU 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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47A ILE* 3.5 23.8 - - + -
48A PRO* 4.5 11.7 - - + +
50A LEU* 4.2 11.9 - - + -
54A LEU* 5.1 10.5 - - + -
58A LEU* 3.8 28.3 - - + -
72A ALA* 4.4 7.6 - - + +
75A LEU* 3.8 26.2 - - + -
76A SER* 2.7 38.3 + - - +
79A LEU* 4.1 10.3 - - + -
80A ILE* 3.9 1.6 - - - +
106A ASN 3.2 12.0 + - - +
107A TYR 3.1 7.3 + - - +
109A ASP* 1.3 81.3 - - + +
111A VAL* 1.3 61.4 + - - +
112A ALA 3.5 0.7 - - - -
113A ARG* 3.8 7.3 - - - +
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Residues in contact with VAL 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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79A LEU* 4.0 18.6 - - + +
80A ILE* 3.7 12.6 - - + +
83A LEU* 3.6 26.2 - - + -
107A TYR* 3.0 49.8 + - + +
108A PHE* 3.2 5.1 + - - +
110A LEU* 1.3 77.8 - - - +
112A ALA* 1.3 54.5 + - - +
113A ARG* 3.3 2.0 + - - -
117A THR* 2.7 36.2 + - + +
159A PHE* 4.9 4.5 - - + -
163A ILE* 4.0 16.2 - - + -
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Residues in contact with ALA 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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58A LEU* 5.6 2.1 - - - +
108A PHE 3.1 16.0 + - - +
109A ASP* 4.2 11.1 - - - +
110A LEU 3.5 0.4 - - - -
111A VAL* 1.3 76.7 - - - +
113A ARG* 1.3 59.7 + - - +
117A THR* 3.5 4.7 - - - -
118A PHE* 4.0 6.5 - - + -
159A PHE* 3.9 21.1 - - + -
162A PHE* 4.4 17.7 - - + -
163A ILE* 4.6 3.1 - - + -
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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