Contacts of the strand formed by residues 43 - 51 (chain B) in PDB entry 1NMS
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 GLU 43 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41B TYR* 3.9 4.0 - - - +
42B PRO* 1.3 85.2 - - + +
44B MET* 1.3 60.1 + - - +
45B GLY* 4.1 5.1 - - - +
82B LYS 5.6 0.4 - - - -
84B GLU* 4.1 12.3 - - - +
110B LYS* 3.0 24.1 + - - +
111B ARG* 3.3 38.6 + - + +
112B SER* 2.8 30.0 + - - -
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Residues in contact with MET 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B MET* 3.6 33.2 - - + +
43B GLU* 1.3 72.1 - - - +
45B GLY* 1.3 55.2 + - - +
81B LEU 3.4 18.8 - - - +
82B LYS* 3.4 31.5 + - + +
83B TYR* 3.7 26.9 - - + +
112B SER* 3.3 3.2 + - - -
113B SER* 2.7 38.7 + - - -
275B PHE* 3.8 29.4 - - + +
277B HIS* 3.5 29.6 - - + +
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Residues in contact with GLY 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B GLU* 3.3 5.6 - - - +
44B MET* 1.3 80.0 - - - +
46B LEU* 1.3 66.3 + - - -
82B LYS 4.7 1.0 + - - -
83B TYR* 3.2 8.7 - - - -
84B GLU* 2.9 26.4 + - - +
111B ARG* 3.8 20.0 - - - -
113B SER 3.4 11.0 - - - -
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Residues in contact with LEU 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B GLY* 1.3 74.2 - - - -
47B CYS* 1.3 60.7 + - - +
48B ILE* 4.2 9.4 - - + -
83B TYR* 3.7 3.0 - - - -
84B GLU* 3.5 41.3 - - + +
86B ARG* 3.6 26.7 - - - +
103B VAL* 3.8 23.6 - - + -
106B GLU* 3.7 19.1 - - - +
108B HIS* 4.1 4.9 - - + -
111B ARG* 3.7 23.9 - - - +
113B SER 4.1 4.0 + - - -
114B PHE* 3.8 12.2 - - + +
115B VAL* 2.9 27.7 + - - +
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Residues in contact with CYS 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B LEU* 1.3 72.1 - - - +
48B ILE* 1.3 62.5 + - - +
49B ILE* 3.7 21.6 + - - -
78B PHE* 3.7 30.3 - - + -
83B TYR* 3.8 21.1 - - + -
84B GLU 2.9 9.7 + - - -
85B VAL* 3.3 10.6 - - + +
86B ARG 2.9 25.8 + - - +
115B VAL* 3.3 23.8 - - + -
117B VAL* 4.2 4.5 - - - -
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Residues in contact with ILE 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B LEU* 4.2 11.0 - - + -
47B CYS* 1.3 72.8 - - - +
49B ILE* 1.3 57.6 + - - +
50B ILE* 4.2 10.3 - - + -
86B ARG* 3.6 38.8 - - + +
88B LYS* 5.1 2.5 - - + -
99B LEU* 4.1 19.3 - - + -
100B MET* 4.0 21.8 - - + -
103B VAL* 4.1 20.9 - - + -
114B PHE* 3.9 26.7 - - + -
115B VAL 2.9 9.8 + - - +
116B CYS* 3.4 4.8 - - - -
117B VAL* 2.7 34.1 + - - +
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Residues in contact with ILE 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B CYS* 4.0 15.3 - - - -
48B ILE* 1.3 75.3 - - - +
50B ILE* 1.3 63.0 + - - +
51B ASN* 4.7 1.8 - - + +
71B ALA* 4.1 7.0 - - + +
74B LEU* 3.7 25.6 - - + -
75B ARG* 3.8 9.9 - - - +
85B VAL* 3.6 26.7 - - + -
86B ARG 3.0 7.3 + - - +
87B ASN* 3.6 26.2 - - - +
88B LYS* 2.8 30.3 + - - +
117B VAL* 3.6 16.6 - - + -
119B LEU* 4.2 24.7 - - + -
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Residues in contact with ILE 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B ILE* 4.2 13.2 - - + -
49B ILE* 1.3 74.4 - - - +
51B ASN* 1.3 61.4 + - - +
52B ASN* 3.9 18.8 - - - +
88B LYS* 3.6 3.1 - - + +
91B LEU* 4.2 11.7 - - + -
96B ILE* 3.9 42.0 - - + -
99B LEU* 4.0 22.4 - - + -
100B MET* 4.2 11.7 - - + -
116B CYS* 5.1 0.2 - - - -
117B VAL 2.8 13.8 + - - +
118B LEU* 3.6 27.4 - - + -
119B LEU* 2.9 33.2 + - - +
120B SER* 6.5 0.2 - - - -
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Residues in contact with ASN 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ILE* 3.7 4.2 + - + -
50B ILE* 1.3 73.3 - - - +
52B ASN* 1.3 59.8 + - - +
53B LYS* 3.7 3.5 + - - +
67B THR* 2.6 36.6 + - - +
68B ASP* 3.0 26.3 + - - -
71B ALA* 3.7 25.7 - - + +
87B ASN* 5.3 1.1 - - - +
88B LYS 2.8 8.1 + - - +
89B ASN* 3.1 30.9 + - - +
90B ASP* 3.0 19.8 + - - +
119B LEU* 3.7 7.1 - - + +
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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