Contacts of the strand formed by residues 63 - 68 (chain A) in PDB entry 1LAN
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 SER 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A LYS 4.8 0.6 + - - -
3A GLY* 3.8 4.3 - - - -
4A LEU 3.4 21.0 + - - +
53A THR* 4.6 1.8 - - - -
54A PHE 3.7 3.4 - - - -
55A TYR* 3.4 25.2 - - - -
61A PHE 3.1 1.8 - - - +
62A PRO* 1.3 80.8 - - - +
64A VAL* 1.3 64.4 + - - +
65A VAL 4.2 0.2 - - - -
100A ILE* 4.3 5.4 - - - +
103A LEU* 3.8 14.8 - - - +
105A ILE* 3.7 30.3 - - - +
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Residues in contact with VAL 64 (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 LEU* 3.5 15.5 - - + +
6A LEU* 4.1 25.8 - - + -
27A PHE* 4.1 18.8 - - + -
35A LEU* 4.5 9.6 - - + -
52A ARG 3.8 1.0 - - - +
53A THR* 3.4 2.1 - - - +
54A PHE* 2.8 44.4 + - + +
57A LEU* 4.4 11.4 - - + -
61A PHE* 3.8 27.4 - - + +
63A SER* 1.3 77.7 - - - +
65A VAL* 1.3 63.4 + - - +
66A VAL* 4.0 14.2 + - + -
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Residues in contact with VAL 65 (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 LEU 2.9 11.0 + - - +
5A VAL* 3.3 10.2 - - + +
6A LEU 2.9 24.3 + - - -
51A THR* 3.9 25.1 - - - +
52A ARG 3.4 8.7 - - - +
53A THR* 3.4 25.8 - - + +
64A VAL* 1.3 73.7 - - - +
66A VAL* 1.3 61.8 + - - +
67A VAL* 3.9 1.7 + - + -
96A GLY* 3.9 21.8 - - - +
99A GLN* 3.8 12.8 - - + -
100A ILE* 3.7 28.7 - - + -
103A LEU* 5.2 0.2 - - + -
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Residues in contact with VAL 66 (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* 3.1 15.5 - - + +
8A ILE* 3.8 23.1 - - + -
20A PHE* 4.5 9.2 - - + -
35A LEU* 4.0 25.6 - - + -
39A LEU* 4.9 4.3 - - + -
46A LEU* 3.6 23.9 - - + +
51A THR* 3.3 5.0 - - - -
52A ARG 2.9 32.2 + - - +
54A PHE* 3.9 23.6 - - + -
64A VAL* 4.4 6.7 - - + -
65A VAL* 1.3 74.1 - - - +
67A VAL* 1.3 63.2 + - - +
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Residues in contact with VAL 67 (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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5A VAL* 4.0 16.2 - - + -
6A LEU 2.7 20.0 + - - +
7A GLY* 3.3 8.2 - - - -
8A ILE* 2.9 30.0 + - - +
46A LEU* 4.8 0.4 - - - -
50A LYS 3.5 5.4 - - - +
51A THR* 3.6 17.7 - - + -
65A VAL* 4.1 2.9 - - + -
66A VAL* 1.3 78.6 - - - +
68A GLY* 1.3 59.1 + - - +
69A LEU* 3.6 5.3 + - + -
92A ALA* 3.4 42.6 - - + +
93A VAL* 4.5 3.8 - - + +
96A GLY* 3.7 15.0 - - - -
113A CYS* 5.2 1.6 - - - -
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Residues in contact with GLY 68 (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 ILE 3.5 6.1 - - - -
46A LEU* 4.2 14.8 - - - +
47A LYS 3.6 18.8 - - - -
48A ALA* 3.6 1.6 - - - -
49A GLY 3.0 22.8 + - - -
50A LYS 2.9 13.3 + - - -
67A VAL* 1.3 70.3 - - - +
69A LEU* 1.3 61.1 + - - -
70A GLY 3.5 3.1 - - - -
88A ASN 4.7 0.5 - - - +
92A ALA* 3.3 11.5 - - - +
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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