Contacts of the strand formed by residues 97 - 113 (chain A) in PDB entry 1NT3
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 VAL 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A LEU* 4.0 27.8 - - + -
89A LEU* 4.9 7.4 - - + -
90A THR 3.3 6.5 - - - +
91A SER* 4.0 14.6 - - - -
94A ASN* 5.0 2.9 - - - +
95A LYS 3.9 7.2 + - - +
96A LEU* 1.3 92.5 - - + +
98A GLY* 1.3 59.2 + - - +
100A ARG* 4.3 1.6 - - - -
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Residues in contact with GLY 98 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A ALA 3.4 0.2 - - - +
89A LEU* 3.9 13.5 - - - +
90A THR* 2.7 44.1 + - - +
97A VAL* 1.3 77.7 - - - +
99A TRP* 1.3 59.7 + - - -
100A ARG* 3.9 7.7 - - - +
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Residues in contact with TRP 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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41A ILE* 4.1 37.7 - - + -
50A GLN* 4.2 1.8 - - - -
87A ARG* 3.1 57.9 + - + +
88A ALA* 3.3 29.2 - - - -
89A LEU* 3.4 34.5 - - + +
98A GLY* 1.3 72.2 - - - -
100A ARG* 1.3 66.0 + - - +
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Residues in contact with ARG 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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29A ASP* 4.0 31.0 - - - +
31A ARG* 4.2 9.3 - - - +
35A VAL* 4.4 5.3 - - - +
87A ARG* 3.5 5.7 - - - +
88A ALA* 2.9 31.1 + - - +
90A THR* 2.8 47.7 + - + +
91A SER* 3.6 7.0 - - - +
92A GLU* 3.5 32.4 + - - +
96A LEU 3.4 19.4 + - - -
97A VAL 4.3 0.4 - - - -
98A GLY* 3.9 11.1 + - - +
99A TRP* 1.3 79.7 - - - +
101A TRP* 1.3 64.0 + - - +
102A ILE* 3.5 1.6 + - + +
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Residues in contact with TRP 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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29A ASP* 3.5 8.8 - - - +
30A ILE* 3.3 51.6 + - + +
85A TYR* 3.8 27.8 - - + -
86A VAL* 3.4 30.7 - - - -
87A ARG* 3.3 54.8 - - + +
100A ARG* 1.3 74.3 - - - +
102A ILE* 1.3 59.1 + - - +
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Residues in contact with ILE 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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24A LYS* 4.8 1.6 - - + -
27A ALA* 4.1 25.6 - - + -
28A ILE 3.5 8.5 - - - +
29A ASP* 4.3 4.3 - - - +
35A VAL* 4.1 10.1 - - + -
37A VAL* 4.5 6.3 - - + -
52A PHE* 3.8 10.1 - - + -
84A THR 3.5 2.3 - - - +
85A TYR* 3.6 5.0 - - - -
86A VAL 2.9 31.6 + - - +
88A ALA* 3.2 24.7 - - + -
90A THR* 4.1 21.3 - - + -
100A ARG 3.5 3.8 + - - +
101A TRP* 1.3 77.1 - - - +
103A ARG* 1.3 60.8 + - - +
104A ILE* 3.7 27.1 + - + +
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Residues in contact with ARG 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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24A LYS* 4.8 4.0 - - - -
27A ALA* 4.8 5.4 - - - +
28A ILE* 2.9 32.2 + - + +
29A ASP 4.4 6.7 - - - +
83A GLN* 3.0 59.9 + - + +
84A THR* 3.5 6.4 + - - +
85A TYR* 3.9 30.2 + - + -
102A ILE* 1.3 74.6 - - - +
104A ILE* 1.3 68.8 + - - +
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Residues in contact with ILE 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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24A LYS* 3.8 15.7 - - - +
52A PHE* 3.5 35.7 - - + -
53A TYR 4.7 4.7 - - - +
54A GLU* 3.5 24.0 - - + -
83A GLN* 3.1 9.8 - - - +
84A THR* 3.0 30.9 + - + +
86A VAL* 4.1 19.1 - - + -
102A ILE* 3.7 24.2 - - + +
103A ARG* 1.3 86.0 - - - +
105A ASP* 1.3 78.1 + - - +
106A THR* 3.3 3.6 + - - -
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Residues in contact with ASP 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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53A TYR 4.5 1.0 - - - +
54A GLU* 3.5 21.2 + - + +
55A THR 3.4 28.6 + - - +
56A ARG* 4.4 11.2 - - + +
81A THR* 3.0 27.1 + - - -
82A SER 3.6 6.5 - - - +
83A GLN* 3.5 21.9 + - - +
104A ILE* 1.3 86.0 - - - +
106A THR* 1.3 59.8 + - - +
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Residues in contact with THR 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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53A TYR 5.8 0.7 + - - -
54A GLU* 5.3 0.2 - - - +
55A THR* 3.0 25.8 + - - +
82A SER* 2.8 20.4 + - - +
83A GLN 3.9 4.0 - - - +
84A THR* 3.4 41.5 - - + +
104A ILE* 3.9 0.9 - - - -
105A ASP* 1.3 76.0 - - - +
107A SER* 1.3 68.0 + - - +
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Residues in contact with SER 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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55A THR* 3.0 21.2 + - - +
81A THR* 3.3 5.7 - - - -
82A SER* 2.9 40.8 + - - +
106A THR* 1.3 85.2 - - - +
108A CYS* 1.3 63.9 + - - +
109A VAL* 3.6 10.8 - - - +
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Residues in contact with CYS 108 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A VAL* 6.0 0.7 - - - +
14A CYS* 3.6 33.3 - - + +
15A ASP 3.7 5.6 - - - -
16A SER* 3.8 24.0 - - - -
57A CYS* 2.0 51.4 - - - +
79A CYS* 3.9 4.7 - - - -
80A LYS 3.5 2.9 - - - -
107A SER* 1.3 77.8 - - - +
109A VAL* 1.3 62.9 + - - +
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Residues in contact with VAL 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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14A CYS* 4.0 3.6 - - - -
78A GLN 3.6 0.2 - - - +
79A CYS* 3.2 1.2 - - - -
80A LYS* 2.6 52.4 + - + +
82A SER* 3.3 28.0 - - - +
107A SER* 3.6 13.9 - - - +
108A CYS* 1.3 79.0 - - - +
110A CYS* 1.3 65.5 + - - +
111A ALA* 3.7 3.7 + - + +
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Residues in contact with CYS 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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13A VAL* 4.1 16.4 - - + +
14A CYS* 3.6 10.9 - - - -
67A CYS* 2.0 47.8 - - + -
70A ILE* 4.1 4.5 - - - -
77A SER* 3.9 11.2 - - - -
78A GLN 3.5 3.4 - - - -
109A VAL* 1.3 74.6 - - - +
111A ALA* 1.3 60.0 + - - +
112A LEU* 3.9 15.9 + - - +
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Residues in contact with ALA 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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76A ASN 3.8 0.2 - - - +
77A SER* 3.1 7.1 - - - -
78A GLN* 2.7 42.8 + - + +
80A LYS* 5.3 9.2 - - + -
109A VAL* 3.7 6.8 + - + +
110A CYS* 1.3 72.5 - - - +
112A LEU* 1.3 61.2 + - - +
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Residues in contact with LEU 112 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A ILE* 4.4 9.4 - - + -
75A TRP* 3.7 46.0 - - + -
76A ASN 3.2 2.2 - - - +
77A SER* 3.6 24.7 - - - -
110A CYS* 3.9 16.3 + - - +
111A ALA* 1.3 76.1 - - - +
113A SER* 1.3 60.1 + - - +
114A ARG* 3.8 12.1 + - - -
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Residues in contact with SER 113 (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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75A TRP* 2.9 24.1 - - - -
76A ASN* 2.4 55.3 + - - +
112A LEU* 1.3 70.5 - - - +
114A ARG* 1.3 87.4 + - - +
115A LYS* 4.4 0.9 + - - -
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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