Contacts of the strand formed by residues 74 - 79 (chain B) in PDB entry 3SN5
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 74 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B CYS 3.7 0.2 - - - +
70B LYS* 3.5 3.1 - - - -
71B LEU 2.9 34.3 + - - +
72B MET 3.0 11.4 + - - +
73B GLY* 1.3 77.7 - - - +
75B TYR* 1.4 60.3 + - - +
76B VAL* 3.9 8.2 + - + +
100B PHE* 5.4 9.6 - - + -
384B ASP 5.6 2.0 - - - +
386B ILE* 3.8 28.5 - - + -
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Residues in contact with TYR 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ARG* 3.6 66.5 + - + +
34B LEU* 4.1 12.3 - - + -
36B ASN* 3.6 21.2 + - - -
68B THR* 4.2 7.0 - - + -
69B CYS 3.6 2.2 - - - -
70B LYS* 3.6 37.1 - - + +
73B GLY 3.4 18.2 - - - -
74B LYS* 1.4 70.4 - - - +
76B VAL* 1.3 60.1 + - - +
77B HIS* 4.0 1.1 + - - -
384B ASP 5.8 0.4 + - - -
385B ASP* 3.7 13.1 + - - +
386B ILE* 3.0 25.0 + - - +
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Residues in contact with VAL 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B PHE 3.7 1.0 - - - +
68B THR* 3.1 4.4 - - - -
69B CYS* 2.7 42.7 + - - +
71B LEU* 3.9 23.6 - - + +
74B LYS* 4.4 11.4 - - + +
75B TYR* 1.3 73.6 - - - +
77B HIS* 1.3 62.2 + - - +
78B PHE* 3.7 28.7 + - + -
361B LEU* 6.0 1.6 - - + -
363B ILE* 6.3 0.2 - - + -
386B ILE* 3.4 21.3 - - + -
388B ALA* 3.7 29.2 - - + -
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Residues in contact with HIS 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ARG* 4.3 5.6 - - - -
31B GLU* 6.0 1.3 - - - -
32B PRO* 3.7 22.6 - - + +
66B VAL* 5.5 1.8 - - + -
67B PHE 3.6 5.4 - - - +
68B THR* 2.8 35.1 + - + +
75B TYR 4.2 2.0 - - - -
76B VAL* 1.3 71.8 - - - +
78B PHE* 1.3 60.3 + - - +
79B ILE* 3.8 14.2 - - + +
380B ASN 4.5 3.1 - - - -
381B ILE* 3.6 33.2 - - + +
385B ASP* 2.8 37.3 + - + -
386B ILE 2.8 28.0 + - - +
387B ILE* 3.6 5.3 - - + -
388B ALA 2.8 29.3 + - - +
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Residues in contact with PHE 78 (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 PHE* 4.2 10.1 - + - -
55B PHE* 5.0 1.1 - + - -
56B LEU* 3.7 32.8 - - + -
65B HIS 3.3 13.3 - - - +
66B VAL* 3.5 14.0 - - - +
67B PHE* 2.9 43.9 + + + -
69B CYS* 4.0 15.5 - - + -
71B LEU* 3.7 27.8 - - + -
76B VAL* 3.7 27.1 - - + -
77B HIS* 1.3 71.2 - - - +
79B ILE* 1.3 63.0 + - - +
80B THR* 3.8 6.9 - - + +
361B LEU* 4.2 22.9 - - + -
388B ALA* 3.6 13.7 - - + -
390B TYR* 4.9 6.7 - - + -
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Residues in contact with ILE 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B HIS 3.8 2.9 - - - +
66B VAL* 4.5 21.3 - - + -
77B HIS* 3.8 21.1 - - + +
78B PHE* 1.3 76.1 - - - +
80B THR* 1.3 61.8 + - - +
81B ASN* 4.3 4.7 - - + +
84B SER* 3.9 31.6 - - - -
85B TYR* 3.8 5.9 + - + -
88B VAL* 3.9 18.4 - - + -
374B LEU* 4.9 8.5 - - + -
381B ILE* 6.2 2.9 - - + -
387B ILE* 3.8 22.0 - - + -
388B ALA 3.1 8.5 + - - +
389B LEU* 3.6 37.6 - - + +
390B TYR 4.9 1.7 + - - -
393B LEU* 5.6 0.9 - - - +
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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
------------------------------------------------------------
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