Contacts of the strand formed by residues 15 - 19 (chain B) in PDB entry 3P8P
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 HIS 15 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ALA* 4.6 0.2 - - - +
14B THR* 1.3 110.4 + - - +
16B ALA* 1.3 63.7 + - - +
17B VAL* 5.6 0.7 - - + -
60B LEU* 4.3 6.4 - - - +
61B GLN* 3.0 36.1 - - + +
63B VAL* 4.9 8.7 - - + -
112B LEU* 4.4 30.1 - - + +
278B LEU* 3.7 2.6 - - - +
279B ILE* 2.9 42.7 + - + +
281B LYS* 4.2 24.2 - - + +
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Residues in contact with ALA 16 (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 HIS* 1.3 76.4 - - - +
17B VAL* 1.3 63.8 + - - +
18B VAL* 3.9 1.5 + - + -
54B LEU* 4.1 18.8 - - + -
60B LEU* 3.7 21.1 - - + -
61B GLN 2.8 7.5 + - - -
62B VAL* 3.4 17.3 - - + +
63B VAL 2.9 24.8 + - - -
276B SER* 4.9 2.0 - - - -
277B VAL 3.6 4.9 - - - -
278B LEU* 4.1 11.4 - - + -
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Residues in contact with VAL 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B HIS* 5.6 1.3 - - + -
16B ALA* 1.3 76.0 - - - +
18B VAL* 1.3 69.3 + - - +
63B VAL* 3.8 20.2 - - + +
65B LEU* 4.3 13.2 - - + -
77B VAL* 3.5 3.3 - - - +
105B MET* 3.8 29.6 - - + -
108B ALA* 5.1 5.4 - - + -
109B LEU* 4.8 12.8 - - + -
112B LEU* 5.0 8.7 - - + -
276B SER* 3.2 6.9 - - - -
277B VAL* 2.9 39.3 + - + +
279B ILE* 3.7 22.4 - - + -
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Residues in contact with VAL 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ALA 4.5 1.1 - - - +
17B VAL* 1.3 77.4 - - - +
19B ARG* 1.3 62.9 + - - +
47B HIS* 4.3 8.1 - - + +
50B TYR* 4.2 10.8 - - + -
51B VAL* 4.1 13.5 - - + -
54B LEU* 4.6 4.7 - - + -
62B VAL* 3.8 18.4 - - + -
63B VAL 3.1 9.4 + - - +
64B GLU* 2.9 29.2 - - - +
65B LEU* 2.9 30.8 + - - +
77B VAL* 4.0 6.3 - - - -
275B CYS 2.8 26.0 - - - +
276B SER* 3.7 12.3 - - - -
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Residues in contact with ARG 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B VAL* 1.3 78.7 - - - +
20B ALA* 1.3 74.9 + - - +
47B HIS* 3.4 15.5 + - - -
64B GLU* 5.1 0.7 - - - -
65B LEU* 3.6 17.6 - - + +
66B PRO* 2.7 29.2 + - - +
68B ASP* 3.8 20.4 + - - +
71B LEU* 4.0 9.5 - - - +
74B CYS* 3.3 47.5 - - + +
75B VAL* 3.3 17.2 + - - +
77B VAL* 3.7 12.0 - - + +
100B LYS 5.0 0.2 + - - -
101B GLU* 3.3 26.9 + - - +
104B MET* 3.5 29.8 - - - +
105B MET 5.1 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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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