Contacts of the strand formed by residues 6 - 13 (chain A) in PDB entry 1BWN
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 LEU 6 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A VAL* 3.1 10.1 - - - +
5A ILE* 1.3 86.3 - - + +
7A GLU* 1.3 62.1 + - - +
31A LEU* 3.5 0.3 - - - -
32A LEU* 3.0 31.4 + - + -
120A LEU* 6.3 0.4 - - + -
123A ARG* 3.9 28.5 - - + +
124A TRP* 3.5 53.6 - - + +
127A GLN* 3.5 39.3 - - + -
89B MET* 5.2 0.2 - - - -
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Residues in contact with GLU 7 (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 VAL* 4.0 13.3 - - + +
6A LEU* 1.3 80.3 - - - +
8A SER* 1.3 68.2 + - - +
29A LEU* 3.8 16.5 - - + +
30A PHE 3.3 5.6 - - - +
31A LEU* 3.4 33.6 - - + +
49A ARG* 5.5 0.9 + - - -
124A TRP* 3.7 0.9 - - - -
88B GLU 5.4 4.0 - - - +
89B MET* 2.7 40.6 - - + +
92B ILE* 3.8 21.0 - - + +
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Residues in contact with SER 8 (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* 5.7 0.3 - - - +
7A GLU* 1.3 81.0 + - - +
9A ILE* 1.3 62.8 + - - +
10A PHE* 3.9 18.2 - - - -
29A LEU* 3.5 5.3 - - - +
30A PHE* 2.7 37.1 + - - +
120A LEU* 3.9 11.8 - - - +
124A TRP* 2.8 33.5 + - - -
91B GLN* 3.5 13.4 + - - -
92B ILE* 3.9 4.7 - - - -
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Residues in contact with ILE 9 (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* 1.3 74.3 - - - +
10A PHE* 1.3 76.0 + - - +
27A LYS* 4.6 3.8 - - + -
28A ARG 3.4 9.6 - - - +
29A LEU* 4.1 15.0 - - + -
42A TYR* 4.0 21.5 - - + -
95A ILE* 4.4 9.4 - - + -
98A PHE* 3.5 19.7 - - + -
116A PRO* 4.1 0.2 - - - +
44B PHE* 3.9 26.0 - - + -
91B GLN* 2.8 40.7 + - + +
92B ILE* 3.9 21.3 - - + +
95B ILE* 4.0 24.9 - - + -
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Residues in contact with PHE 10 (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* 3.9 8.1 - - - -
9A ILE* 1.3 81.9 - - - +
11A LEU* 1.3 61.3 + - - +
26A LYS 3.9 0.2 - - - +
27A LYS* 3.3 3.9 - - - +
28A ARG* 2.8 31.5 + - - +
30A PHE* 3.6 26.2 - + + -
98A PHE* 4.0 6.7 - - - -
102A PHE* 3.9 15.0 - + - -
113A VAL* 3.5 28.3 - - + -
114A PHE 3.7 13.9 - - - +
115A SER* 3.5 28.0 - - - -
116A PRO* 3.8 4.9 - - + -
120A LEU* 4.0 8.5 - - + -
124A TRP* 3.4 59.5 - + - -
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Residues in contact with LEU 11 (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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10A PHE* 1.3 74.0 - - - +
12A LYS* 1.3 58.4 + - - +
25A PHE* 3.8 26.7 - - + +
26A LYS* 3.5 24.0 - - - +
27A LYS* 3.9 12.1 - - + +
76A GLU* 4.0 20.0 - - - +
77A ARG* 3.6 37.5 - - + -
98A PHE* 3.5 33.1 - - + -
113A VAL* 3.5 1.2 - - - +
114A PHE* 2.6 41.6 + - + -
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Residues in contact with LYS 12 (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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1A 4IP 2.9 51.8 + - - +
10A PHE 4.1 0.2 + - - -
11A LEU* 1.3 74.9 - - - +
13A ARG* 1.3 72.5 + - - +
14A SER* 3.9 3.8 - - - +
25A PHE* 3.3 7.7 - - - -
26A LYS* 2.9 40.3 + - + +
28A ARG* 4.0 7.6 - - + -
30A PHE* 3.9 24.7 - - + -
39A TYR* 3.5 40.8 - - + -
111A LEU* 4.0 10.8 - - + -
112A TYR 3.2 14.1 - - - +
113A VAL* 4.5 0.7 - - - -
114A PHE* 4.6 0.4 - - - -
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Residues in contact with ARG 13 (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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12A LYS* 1.3 87.2 + - - +
14A SER* 1.3 72.7 + - - +
15A GLN* 3.4 5.5 + - - +
23A LEU* 3.5 34.3 - - + +
24A ASN 3.4 6.3 - - - +
25A PHE* 3.8 36.0 - - + -
111A LEU* 4.4 4.2 - - - +
112A TYR* 3.0 52.2 + - + -
114A PHE* 4.6 1.1 - - - -
146A PHE* 4.1 18.5 - - - +
147A TRP* 2.7 44.0 + - - +
148A ILE* 3.3 18.1 - - - +
160A LYS* 5.6 2.4 - - - +
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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