Contacts of the strand formed by residues 30 - 34 (chain B) in PDB entry 5F71
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 VAL 30 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B TYR* 4.2 8.1 - - + +
27B LEU* 6.4 0.7 - - + -
28B VAL 3.7 9.4 - - - +
29B PRO* 1.3 82.0 - - - +
31B CYS* 1.3 62.4 + - - +
32B TRP* 4.1 20.0 - - + -
47B LEU* 3.7 1.8 - - + +
48B ARG* 3.5 7.9 - - - +
49B THR* 2.7 44.7 + - + +
63B LEU* 5.1 0.9 - - + -
72B VAL* 3.7 42.0 - - + -
89B CYS* 4.4 5.4 - - - -
90B ARG 3.2 6.5 - - - +
91B ILE* 3.9 16.2 - - + -
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Residues in contact with CYS 31 (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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30B VAL* 1.3 73.5 - - - +
32B TRP* 1.3 62.2 + - - +
41B GLU* 3.7 20.0 - - - -
42B CYS* 2.0 46.1 - - + +
45B VAL* 4.3 8.7 - - - -
47B LEU 3.9 1.3 - - - -
48B ARG* 4.4 13.5 - - - -
88B CYS 3.1 4.7 - - - +
89B CYS* 3.4 1.2 - - - -
90B ARG* 2.7 52.0 + - + +
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Residues in contact with TRP 32 (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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15B LEU* 3.6 34.5 - - + -
17B CYS* 3.5 16.6 - - + -
30B VAL* 4.1 14.6 - - + +
31B CYS* 1.3 74.3 - - - +
33B GLY* 1.3 58.0 + - - +
42B CYS* 3.7 6.5 - - - -
45B VAL* 3.7 0.2 - - - -
46B VAL* 2.9 38.2 + - + -
47B LEU* 2.9 23.6 + - + +
63B LEU* 4.1 16.8 - - + +
72B VAL 2.7 29.7 + - - -
74B LEU* 3.5 26.2 - - + +
87B TYR* 3.8 27.8 - + + -
88B CYS 3.2 15.9 - - - -
89B CYS* 3.8 12.2 - - + -
104B LEU* 3.5 28.7 - - + -
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Residues in contact with GLY 33 (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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32B TRP* 1.3 76.0 - - - +
34B LYS* 1.3 61.9 + - - -
35B GLY 3.8 0.2 - - - -
42B CYS* 3.5 22.6 - - - +
44B ASN 3.3 11.7 - - - -
46B VAL* 4.2 1.8 - - - -
87B TYR* 3.3 12.7 - - - -
88B CYS 2.8 34.0 + - - -
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Residues in contact with LYS 34 (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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33B GLY* 1.3 70.0 - - - -
35B GLY* 1.3 62.3 + - - +
42B CYS 4.6 1.3 - - - +
43B GLY* 5.0 0.7 - - - -
44B ASN* 3.0 51.3 + - + +
46B VAL* 4.6 8.8 - - + +
82B ALA 3.3 19.8 + - - -
83B ASP* 3.9 3.4 + - - +
84B SER 2.9 29.6 + - - -
85B GLY* 3.9 13.2 - - - -
86B ILE 3.7 4.7 - - - +
87B TYR* 3.5 31.2 + - + +
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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