Contacts of the strand formed by residues 14 - 19 (chain A) in PDB entry 4BN2
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 LYS 14 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A ALA 4.6 5.8 - - - +
13A ILE* 1.3 77.5 - - - +
15A VAL* 1.3 60.5 + - - +
16A PHE* 3.6 27.8 - - + -
59A ASP* 3.3 18.2 - - + +
78A SER* 4.0 23.3 + - - -
79A ILE* 5.4 10.7 - - - +
320A THR 3.1 11.8 + - - +
321A ALA* 3.2 5.0 - - + +
322A ILE* 2.7 32.6 + - - +
347A LYS* 4.7 1.1 - - - +
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Residues in contact with VAL 15 (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 ILE* 4.1 11.2 - - + -
14A LYS* 1.3 77.9 - - - +
16A PHE* 1.3 70.0 + - - +
58A PHE* 3.6 22.9 - - + +
59A ASP* 2.8 41.0 + - - +
322A ILE* 3.5 15.3 - - + +
324A ALA* 5.1 0.2 - - + -
343A ALA* 3.7 25.4 - - + +
346A ALA* 4.2 3.1 - - + -
347A LYS* 3.3 45.8 - - + +
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Residues in contact with PHE 16 (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 LYS* 3.6 39.9 - - + -
15A VAL* 1.3 75.1 - - - +
17A VAL* 1.3 65.3 + - - +
18A ARG 4.2 0.4 - - - -
58A PHE* 4.8 0.2 - - - -
59A ASP* 3.8 16.4 - - + -
60A HIS* 3.5 30.7 - - + +
74A THR* 3.7 36.1 - - + -
75A VAL* 3.6 31.6 - - + -
321A ALA* 4.1 12.1 - - + -
322A ILE 2.9 14.8 + - - +
323A ILE* 4.4 6.7 - - + -
324A ALA* 2.8 29.7 + - - +
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Residues in contact with VAL 17 (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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16A PHE* 1.3 79.7 - - - +
18A ARG* 1.3 64.5 + - - +
19A ILE* 4.4 4.7 - - + -
45A LEU* 4.1 20.4 - - + -
58A PHE* 3.5 43.3 - - + -
60A HIS 3.1 9.6 + - - +
61A VAL* 3.5 7.1 - - + -
62A ALA* 2.9 27.7 + - - +
324A ALA* 3.4 16.8 - - + +
326A VAL* 4.1 18.8 - - + -
340A LEU* 4.3 11.2 - - + -
343A ALA* 5.2 0.2 - - + -
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Residues in contact with ARG 18 (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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16A PHE 4.2 0.2 - - - -
17A VAL* 1.3 74.6 - - - +
19A ILE* 1.3 72.1 + - - +
20A ARG* 3.7 2.9 + - + +
62A ALA* 3.7 14.8 - - + +
63A ASP 5.3 1.7 + - - +
66A THR* 3.2 27.9 + - - -
67A THR 4.1 2.8 - - - -
68A GLN* 2.9 30.9 + - - +
71A VAL* 3.5 27.0 - - + +
99A SER 5.2 0.3 - - - +
103A PHE* 3.9 6.7 - - - -
104A THR* 3.0 38.4 + - - +
323A ILE* 4.3 9.6 - - + +
324A ALA 3.0 7.9 + - - -
325A ASN* 3.5 15.2 + - - +
326A VAL 3.1 23.6 + - - +
600A ADP 3.4 24.9 + - - -
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Residues in contact with ILE 19 (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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17A VAL* 4.4 7.2 - - + -
18A ARG* 1.3 78.7 + - - +
20A ARG* 1.3 61.5 + - - +
21A PRO* 4.2 0.3 - - - +
37A LEU* 4.0 20.0 - - + -
39A VAL* 3.6 32.1 - - + +
45A LEU* 4.7 4.0 - - + -
61A VAL* 4.5 7.2 - - + -
62A ALA 2.9 16.2 + - - +
63A ASP* 3.6 7.9 - - - +
64A VAL* 3.2 28.8 + - + -
326A VAL* 3.4 17.7 - - + +
328A PRO* 3.5 42.0 - - + -
600A ADP 5.6 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