Contacts of the strand formed by residues 101 - 112 (chain A) in PDB entry 3NSH
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 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A ASP 3.4 0.9 - - - +
90A LEU* 3.2 6.5 - - - -
91A VAL* 2.6 42.9 + - + +
99A VAL* 4.5 1.6 - - + -
100A THR* 1.3 82.5 - - - +
102A ARG* 1.3 60.4 + - - +
103A ALA* 3.7 10.4 + - + -
142A PHE* 3.8 32.3 - - + -
146A LEU* 3.8 36.6 - - + +
149A GLN* 3.8 18.8 - - + +
150A THR* 3.9 20.6 - - + -
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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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65A THR* 2.7 49.1 + - - +
67A ARG* 3.6 43.3 - - - +
88A THR* 2.9 48.2 + - + +
89A ASP* 3.2 8.5 - - - +
90A LEU* 3.9 21.9 - - + +
101A VAL* 1.3 73.3 - - - +
103A ALA* 1.3 61.6 + - - +
145A SER* 3.9 4.9 + - - -
149A GLN* 2.9 37.3 + - - +
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Residues in contact with ALA 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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44A PHE* 4.8 0.4 - - + -
88A THR* 3.2 6.7 - - - -
89A ASP 2.9 29.2 + - - +
91A VAL* 4.1 12.8 - - + -
101A VAL* 3.7 6.7 + - + -
102A ARG* 1.3 77.1 - - - +
104A ASN* 1.3 70.4 + - - +
105A ILE* 3.5 2.6 + - - +
142A PHE* 3.8 32.5 - - + -
145A SER* 4.4 11.7 - - - +
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Residues in contact with ASN 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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44A PHE* 3.4 26.8 - - - +
69A LEU* 3.5 29.3 - - - +
86A LEU* 5.7 0.7 - - + -
87A GLY 3.6 2.5 - - - +
88A THR* 3.6 10.5 - - - +
103A ALA* 1.3 76.5 - - - +
105A ILE* 1.3 58.1 + - - +
139A LEU* 3.6 29.2 - - + +
140A GLU* 3.0 44.7 + - - +
142A PHE* 5.4 2.4 + - - +
145A SER* 4.9 2.2 + - - -
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Residues in contact with ILE 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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26A VAL* 4.2 10.8 - - + -
44A PHE* 3.6 25.4 - - + +
46A VAL* 3.9 22.4 - - + +
58A TYR* 4.1 17.7 - - + +
66A TYR* 6.6 0.2 - - + -
86A LEU* 3.7 5.5 - - - -
87A GLY* 3.0 33.9 + - - +
88A THR 4.6 0.2 - - - -
89A ASP* 3.5 38.8 - - + +
91A VAL* 3.9 17.0 - - + -
103A ALA 3.8 1.6 - - - +
104A ASN* 1.3 76.9 - - - +
106A ALA* 1.3 74.3 + - - +
107A ALA* 3.5 2.0 + - + +
139A LEU* 6.3 0.2 - - - -
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Residues in contact with ALA 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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43A ASN* 5.5 2.2 - - - +
44A PHE 2.9 13.0 + - - +
45A ALA* 3.2 5.2 - - + +
46A VAL 2.8 28.9 + - - -
73A VAL* 3.7 14.6 - - + -
82A TRP* 3.4 40.8 - - + -
85A GLU 3.5 5.2 - - - -
86A LEU* 4.2 7.5 - - + +
105A ILE* 1.3 70.9 - - - +
107A ALA* 1.3 60.3 + - - +
108A ILE 3.2 3.5 + - - -
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Residues in contact with ALA 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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46A VAL* 3.8 3.1 - - - -
48A ALA* 3.5 22.4 - - + -
58A TYR* 4.5 6.3 - - + -
60A ARG* 3.6 37.0 - - - +
66A TYR* 5.7 0.9 - - + -
84A GLY* 3.2 4.3 - - - -
85A GLU 2.8 37.4 + - - +
105A ILE* 3.5 5.7 + - - +
106A ALA* 1.3 69.3 - - - +
108A ILE* 1.3 62.2 + - - +
109A THR* 3.3 4.4 + - - +
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Residues in contact with ILE 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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45A ALA* 3.9 12.6 - - + -
46A VAL* 2.8 34.0 + - - +
47A GLY* 4.1 2.6 - - - +
48A ALA* 2.9 25.7 + - - -
49A ALA* 3.8 3.1 + - - +
82A TRP* 3.4 37.2 - - + -
83A GLU 3.7 4.7 - - - -
84A GLY* 4.3 0.7 - - - -
106A ALA 3.9 3.4 - - - +
107A ALA* 1.3 69.5 - - - +
109A THR* 1.4 60.6 + - - +
110A GLU 3.7 24.2 - - - +
114A PHE* 3.5 25.1 - - + -
115A PHE* 3.7 22.2 - - + -
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Residues in contact with THR 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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48A ALA* 5.4 1.3 - - + +
49A ALA* 4.3 19.9 - - + +
50A PRO 5.5 1.6 - - - +
60A ARG* 4.3 11.0 - - - +
83A GLU* 3.1 18.7 + - - -
84A GLY* 3.6 6.9 - - - -
85A GLU* 3.7 29.9 + - - +
107A ALA 3.3 12.1 + - - +
108A ILE* 1.4 73.0 - - - +
110A GLU* 1.3 70.0 + - - +
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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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82A TRP* 3.3 3.5 - - - +
83A GLU* 2.8 57.8 + - + +
108A ILE* 3.7 2.9 - - - +
109A THR* 1.3 86.4 + - - +
111A SER* 1.3 63.1 + - - +
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Residues in contact with SER 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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51A HIS* 3.4 32.5 + - - -
81A LYS 3.4 12.6 - - - -
82A TRP* 4.0 6.3 - - - +
108A ILE* 4.4 0.7 - - - -
110A GLU* 1.3 76.0 - - - +
112A ASP* 1.3 62.9 + - - +
114A PHE* 4.0 11.3 + - - +
115A PHE* 3.6 23.6 + - - -
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Residues in contact with ASP 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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79A GLN 5.1 1.2 - - - +
80A GLY* 3.3 1.9 - - - -
81A LYS* 2.9 55.7 + - + +
111A SER* 1.3 77.0 - - - +
113A LYS* 1.3 100.3 + - - +
114A PHE 3.1 0.2 - - - -
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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