Contacts of the strand formed by residues 60 - 65 (chain A) in PDB entry 1I6P
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 60 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A PRO* 3.8 8.4 - - - +
37A PHE* 3.3 13.2 - - + +
39A TRP* 4.4 11.0 - - + -
49A ALA* 4.1 20.4 - - + -
50A GLU* 3.8 33.2 - - + +
55A LEU* 4.2 27.6 - - + -
56A GLU 3.8 16.8 - - - +
57A PRO* 5.0 1.3 - - + -
58A GLY* 3.3 8.1 + - - +
59A GLU* 1.3 84.1 - - - +
61A PHE* 1.3 62.8 + - - +
62A VAL* 3.9 20.2 + - + +
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Residues in contact with PHE 61 (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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35A PRO* 3.8 14.5 - - + +
37A PHE 2.8 12.3 + - - +
38A LEU* 3.4 9.7 - - + +
39A TRP* 2.8 26.0 + - - +
60A LEU* 1.3 74.2 - - - +
62A VAL* 1.3 64.9 + - - +
80A VAL* 3.8 39.5 - - + -
83A TYR* 3.5 33.4 - + + -
84A ALA* 4.0 13.9 - - + -
88A LEU* 3.7 22.0 - - + -
90A VAL* 4.9 2.7 - - + -
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Residues in contact with VAL 62 (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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38A LEU* 4.5 2.2 - - - -
39A TRP* 3.4 17.3 - - + +
49A ALA* 5.8 1.1 - - + -
50A GLU* 4.6 7.6 - - - +
60A LEU* 3.9 32.3 + - + +
61A PHE* 1.3 87.3 - - - +
63A HIS* 1.3 64.8 + - - +
64A ARG* 4.0 33.4 - - + +
80A VAL* 4.9 5.9 - - - +
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Residues in contact with HIS 63 (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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38A LEU* 4.6 0.4 - - + +
39A TRP 2.9 8.9 + - - +
40A ILE* 3.3 17.0 - - + -
41A GLY 3.0 24.3 + - - -
62A VAL* 1.3 74.8 - - - +
64A ARG* 1.3 77.4 + - - +
65A ASN* 3.2 34.3 + - + +
74A ASP* 4.7 1.4 + - - -
76A ASN* 3.1 34.5 + - - -
77A CYS* 3.8 27.7 - - - +
80A VAL* 3.9 29.4 - - + +
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Residues in contact with ARG 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A TRP* 4.1 11.4 - - - +
41A GLY* 3.2 14.8 - - - +
42A CYS 2.9 37.0 + - - +
43A SER* 3.6 12.5 + - - +
45A SER* 3.7 30.7 + - - +
47A VAL 4.7 2.6 + - - -
48A PRO* 4.5 1.6 - - - +
49A ALA* 3.7 35.8 - - - +
50A GLU* 5.4 1.2 + - - -
62A VAL* 4.0 17.4 - - + +
63A HIS* 1.3 90.4 + - - +
65A ASN* 1.3 62.3 + - - +
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Residues in contact with ASN 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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40A ILE* 4.9 1.8 - - - +
41A GLY 3.3 2.4 + - - -
42A CYS* 3.3 5.2 - - - -
43A SER* 2.9 25.7 + - - -
63A HIS* 3.2 30.6 + - + +
64A ARG* 1.3 74.5 - - - +
66A VAL* 1.3 70.0 + - - +
67A ALA 3.1 2.3 + - - -
68A ASN* 3.2 5.0 + - - +
69A LEU 2.8 46.8 + - - +
74A ASP* 4.9 0.4 + - - -
77A CYS* 4.8 2.4 - - - +
119A TRP* 3.7 22.8 - - + -
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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