Contacts of the strand formed by residues 81 - 90 (chain A) in PDB entry 1NPM
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 GLN 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A VAL 3.8 0.4 - - - +
66A ARG* 3.2 7.2 - - - +
67A LEU* 2.9 37.2 + - + +
70A ASP* 5.0 0.2 - - - +
78A GLN 5.1 3.7 + - - +
79A PRO* 3.1 20.4 + - - +
80A GLU* 1.3 76.2 - - - +
82A GLU* 1.3 60.9 + - - +
83A ILE* 4.0 14.5 - - + +
111A SER 4.6 1.0 - - - +
112A ALA* 3.5 12.3 - - - +
113A ASN* 2.9 61.1 + - - +
118A VAL* 4.2 11.7 - - - +
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Residues in contact with GLU 82 (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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34A PHE* 4.8 3.1 - - - +
36A GLY 4.9 5.0 - - - +
64A SER* 2.7 32.4 + - - +
65A VAL 3.3 5.2 - - - +
66A ARG* 3.9 27.9 - - + +
81A GLN* 1.3 75.0 - - - +
83A ILE* 1.3 63.6 + - - +
84A GLN* 4.8 7.2 - - - +
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Residues in contact with ILE 83 (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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64A SER* 3.7 2.5 - - - -
65A VAL* 2.9 37.2 + - + +
67A LEU* 4.2 12.1 - - + -
81A GLN* 4.0 12.8 - - + +
82A GLU* 1.3 83.0 - - - +
84A GLN* 1.3 78.9 + - - +
108A LEU* 4.0 15.0 - - + -
110A ASN* 3.4 38.4 - - + +
111A SER 4.0 6.5 - - - +
112A ALA* 3.8 37.0 - - + -
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Residues in contact with GLN 84 (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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63A TYR 4.9 3.6 + - - -
64A SER* 4.1 21.6 - - - +
82A GLU* 4.8 7.3 - - - +
83A ILE* 1.3 87.3 - - - +
85A VAL* 1.3 65.8 + - - +
108A LEU* 3.6 4.9 - - - +
109A GLN* 2.9 40.6 + - + +
110A ASN* 5.0 5.0 - - - +
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Residues in contact with VAL 85 (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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63A TYR* 3.3 38.9 + - + +
64A SER* 4.6 0.2 - - - -
65A VAL* 3.8 20.2 - - + -
84A GLN* 1.3 77.7 - - - +
86A ALA* 1.3 64.2 + - - +
87A GLN* 3.8 23.3 - - - +
88A SER* 3.8 15.5 - - - +
106A ILE* 3.6 23.6 - - + -
107A ARG 3.9 2.7 - - - -
108A LEU* 5.1 0.2 - - + -
109A GLN* 3.9 7.3 - - - +
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Residues in contact with ALA 86 (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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85A VAL* 1.3 76.2 - - - +
87A GLN* 1.3 59.7 + - + +
107A ARG* 2.8 33.2 + - + +
108A LEU 4.0 0.7 - - - +
109A GLN* 3.7 34.9 - - - +
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Residues in contact with GLN 87 (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 TRP* 5.5 0.3 - - - -
85A VAL* 3.7 6.0 - - - +
86A ALA* 1.3 82.0 - - + +
88A SER* 1.3 66.8 + - - +
89A ILE* 3.8 29.3 - - + +
105A LEU 3.9 0.3 - - - +
106A ILE* 3.4 4.3 - - - -
107A ARG* 2.8 53.1 + - + +
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Residues in contact with SER 88 (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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59A LYS* 3.7 34.5 - - - -
60A LYS 4.8 0.6 + - - -
63A TYR* 2.5 37.9 + - - -
85A VAL* 3.8 5.6 - - - +
87A GLN* 1.3 77.2 - - - +
89A ILE* 1.3 62.7 + - - +
90A GLN 3.9 2.4 + - - -
104A MET* 4.1 6.1 - - - -
105A LEU 4.0 2.5 - - - -
106A ILE* 4.8 1.3 - - - +
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Residues in contact with ILE 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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51A TRP* 4.2 18.4 - - + -
87A GLN* 3.8 37.0 - - + +
88A SER* 1.3 75.9 - - - +
90A GLN* 1.3 69.0 + - - +
92A PRO* 6.2 0.2 - - + -
104A MET* 3.3 5.3 - - - +
105A LEU* 2.9 39.4 + - + +
237A TRP* 3.7 15.8 - - + +
241A THR* 3.8 28.0 - - + +
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Residues in contact with GLN 90 (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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56A ALA* 2.9 30.7 + - + -
59A LYS* 3.6 37.3 + - + +
88A SER 3.9 1.6 + - - -
89A ILE* 1.3 83.4 - - - +
91A HIS* 1.3 72.7 + - - +
92A PRO* 3.3 6.9 - - - +
94A TYR* 3.5 17.4 - - + -
95A ASN* 2.8 35.1 + - - +
103A ILE 3.9 5.4 - - - -
104A MET* 3.7 10.1 - - - -
237A TRP* 3.9 0.8 - - - -
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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