Contacts of the strand formed by residues 64 - 69 (chain B) in PDB entry 4PRO
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 ARG 64 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B THR 3.7 4.0 - - - -
35B GLY* 3.2 7.5 - - - +
57B ARG* 3.3 0.3 - - - -
58B VAL* 2.9 40.6 + - + -
62B ASN* 3.3 31.5 + - + +
63B ASP* 1.3 75.7 - - - +
65B ALA* 1.3 65.2 + - - +
182B GLU* 2.6 30.6 + - - +
186B PRO* 3.9 36.0 + - - +
187B ILE* 3.7 26.1 - - + +
190B GLN* 2.8 37.5 + - - +
191B TYR* 4.0 18.8 - - + +
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Residues in contact with ALA 65 (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 VAL* 3.4 6.9 - - - +
33B THR* 2.9 35.2 + - + +
34B ALA 3.6 20.2 - - - +
35B GLY* 3.7 0.4 - - - -
54B PHE* 4.1 11.0 - - + -
56B ALA 3.4 16.4 - - - +
57B ARG* 3.7 11.0 - - + +
64B ARG* 1.3 78.2 - - - +
66B TRP* 1.3 63.3 + - - +
187B ILE* 4.5 2.6 - - - +
191B TYR* 4.8 5.4 - - - -
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Residues in contact with TRP 66 (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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23B VAL* 4.9 3.1 - - + -
25B ARG* 4.0 43.3 - - + +
28B THR* 4.3 12.1 - - + -
29B LYS 4.4 4.7 - - - -
30B GLY* 4.6 7.0 - - - -
31B PHE 3.3 11.0 - - - +
32B VAL* 4.3 2.5 - - + -
54B PHE* 3.9 1.9 - - - +
55B ALA* 2.9 35.6 + - + +
56B ALA* 3.3 28.4 + - + +
65B ALA* 1.3 78.1 - - - +
67B VAL* 1.3 68.0 + - - +
68B SER* 3.8 32.1 - - - -
191B TYR* 3.5 36.8 - + + +
193B LEU* 4.0 30.7 - - + -
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Residues in contact with VAL 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B GLY* 3.1 21.7 - - - -
31B PHE* 2.9 39.7 + - + +
33B THR* 4.5 2.2 - - + -
44B ALA* 3.9 17.7 - - + -
52B GLY 3.9 2.2 - - - -
53B THR 3.3 32.3 - - - +
54B PHE* 3.9 34.5 - - + -
66B TRP* 1.3 78.1 - - - +
68B SER* 1.3 63.4 + - - +
69B LEU* 3.2 11.6 + - + +
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Residues in contact with SER 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B THR* 4.2 12.3 - - - -
29B LYS 3.6 6.1 - - - -
52B GLY* 3.2 3.0 - - - -
53B THR* 3.1 40.1 + - - -
55B ALA* 3.9 10.8 - - - +
66B TRP* 3.8 26.5 + - - -
67B VAL* 1.3 70.1 - - - +
69B LEU* 1.3 60.7 + - - +
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Residues in contact with LEU 69 (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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3B ILE* 3.6 30.7 - - + -
28B THR* 5.0 3.1 - - - +
29B LYS* 2.8 22.6 + - + +
30B GLY* 3.5 35.0 - - - +
31B PHE* 3.8 21.5 - - + -
51B VAL* 3.1 41.5 - - + +
67B VAL* 3.6 9.0 - - + +
68B SER* 1.3 76.8 - - - +
70B THR* 1.3 67.4 + - - +
71B SER 3.8 0.7 + - - -
73B GLN* 3.6 11.9 - - + -
75B LEU* 3.9 6.3 - - + -
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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