Contacts of the strand formed by residues 61 - 68 (chain B) in PDB entry 5WVD
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 ALA 61 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58B GLY* 3.1 30.6 + - - +
59B ALA 3.8 0.2 - - - -
60B TYR* 1.3 97.1 - - + +
62B LYS* 1.3 61.6 + - - +
78B LYS* 4.1 6.3 - - - -
79B ILE 3.3 11.7 - - - +
80B ILE* 3.9 15.5 - - + -
81B GLU* 5.6 0.2 - - - -
194B LEU* 3.1 25.4 + - + +
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Residues in contact with LYS 62 (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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57A GLU* 3.4 33.8 + - + +
58A GLY 4.9 4.4 + - - -
59A ALA 4.5 4.0 + - - -
60A TYR 5.5 1.4 - - - -
81A GLU* 2.8 36.3 + - - +
54B LEU* 4.0 9.9 - - + -
56B GLY 3.4 14.6 - - - +
61B ALA* 1.3 74.3 - - - +
63B VAL* 1.3 65.2 + - - +
64B GLN* 2.8 30.3 + - + +
78B LYS* 3.4 4.9 - - - +
79B ILE* 2.8 57.1 + - + +
119B ARG* 4.4 4.5 - - - +
194B LEU* 4.1 3.4 - - - -
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Residues in contact with VAL 63 (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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54B LEU* 3.9 2.5 - - - +
55B LEU* 2.8 48.9 + - + -
56B GLY 3.1 13.4 + - - +
62B LYS* 1.3 76.1 - - - +
64B GLN* 1.3 61.5 + - - +
76B ALA* 4.3 4.5 - - + -
77B VAL 3.4 8.3 - - - +
78B LYS* 4.2 7.0 - - + -
192B PHE* 3.8 26.9 - - + -
194B LEU* 3.8 13.2 - - + -
401B 7UX 3.7 43.1 - - + -
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Residues in contact with GLN 64 (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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59A ALA* 2.8 32.6 + - - +
224A PRO* 4.3 0.2 - - - +
50B LEU* 3.6 32.7 - - + +
51B THR 2.7 26.2 + - - +
53B GLU 3.5 15.5 - - - +
54B LEU* 4.4 10.5 - - + -
55B LEU* 4.5 4.9 - - - +
62B LYS* 2.8 35.8 + - + +
63B VAL* 1.3 73.4 - - - +
65B GLY* 1.3 67.2 + - - +
76B ALA* 3.6 0.5 - - - -
77B VAL* 2.8 35.6 + - + +
79B ILE* 5.1 0.7 - - + -
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Residues in contact with GLY 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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50B LEU* 3.7 3.6 - - - +
51B THR* 2.9 37.3 + - - -
53B GLU* 3.1 24.1 + - - -
55B LEU* 4.2 6.9 - - - +
64B GLN* 1.3 77.0 - - - +
66B ALA* 1.3 60.2 + - - +
74B GLU* 5.4 2.5 - - - -
75B TYR 3.4 9.2 - - - -
76B ALA* 4.4 2.9 - - - -
126B LYS* 5.4 1.6 - - - -
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Residues in contact with ALA 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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48B TYR* 4.2 22.9 - - + -
49B LYS 3.4 10.3 - - - +
50B LEU* 4.4 4.3 - - + -
51B THR* 4.4 2.2 - - - +
64B GLN 3.8 0.2 + - - -
65B GLY* 1.3 76.5 - - - +
67B VAL* 1.3 63.5 + - - +
73B LYS 3.9 0.2 - - - +
74B GLU* 3.5 5.7 - - - +
75B TYR* 2.7 46.0 + - + +
77B VAL* 3.9 25.8 - - + -
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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
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221A TYR 6.0 0.4 - - - +
48B TYR* 3.5 3.1 - - - -
49B LYS* 2.7 50.1 + - + +
51B THR* 3.9 20.4 - - + -
66B ALA* 1.3 74.2 - - - +
68B SER* 1.3 74.3 + - - +
69B LEU* 4.3 4.7 - - + +
72B GLY* 4.5 10.5 - - - +
73B LYS 3.7 8.5 - - - +
74B GLU* 4.6 14.6 - - + -
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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
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47B MET 3.7 1.8 + - - -
48B TYR* 3.7 31.0 - - - -
66B ALA 4.0 0.4 - - - -
67B VAL* 1.3 78.5 - - - +
69B LEU* 1.3 56.8 + - - +
70B GLN* 3.1 19.7 + - - +
71B ASN* 3.0 26.9 + - - -
72B GLY* 3.1 23.7 + - - -
73B LYS 3.1 9.9 + - - -
75B TYR* 3.7 12.1 - - - -
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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