Contacts of the strand formed by residues 51 - 56 (chain G) in PDB entry 3QSU
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 51 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47G ASN* 3.5 4.3 - - - -
48G SER 2.9 31.0 + - - +
49G GLN* 2.5 33.9 + - - -
50G GLY* 1.3 94.1 + - - +
52G GLN* 1.3 61.9 + - - +
53G HIS* 3.0 16.9 + - + +
64J THR* 4.3 6.7 - - - +
65J VAL 4.0 19.3 - - - +
66J GLU* 4.1 23.3 - - - +
18M ASN 4.2 0.4 + - - -
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Residues in contact with GLN 52 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37G GLU* 3.1 22.9 - - - +
45G SER* 2.9 20.4 + - - +
47G ASN* 3.7 12.3 + - - +
51G LYS* 1.3 74.1 - - - +
53G HIS* 1.3 56.5 + - - +
54G LEU* 3.6 34.7 - - - +
7J ILE* 5.6 0.8 - - - +
11J ALA* 5.4 5.8 - - - +
15J PHE* 4.8 13.4 - - - -
64J THR* 2.6 33.8 + - - -
65J VAL* 4.3 2.6 + - - +
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Residues in contact with HIS 53 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32G MET* 3.6 23.4 - - + -
44G VAL 3.4 3.6 - - - +
45G SER* 3.4 1.4 - - - -
46G LEU 2.9 44.6 + - - +
48G SER* 3.3 29.7 + - - -
49G GLN* 5.7 0.2 - - + -
51G LYS* 3.0 33.5 + - + -
52G GLN* 1.3 75.8 - - - +
54G LEU* 1.3 60.3 + - - +
55G ILE* 3.7 11.8 + - + +
78G ZN 2.1 37.1 - - - -
25J PHE* 5.7 2.7 - + - -
62J THR* 4.0 11.7 - - + +
63J TYR 3.4 4.3 - - - -
64J THR* 3.8 14.5 + - + -
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Residues in contact with LEU 54 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43G VAL* 3.7 31.6 - - + -
44G VAL 3.7 4.3 - - - +
45G SER* 4.5 2.0 - - - -
52G GLN* 3.6 19.4 - - - +
53G HIS* 1.3 72.2 - - - +
55G ILE* 1.3 59.0 + - - +
56G TYR* 4.2 0.5 + - - -
7J ILE* 3.7 21.3 - - + -
8J GLN* 4.3 15.7 - - + -
11J ALA* 3.9 24.0 - - + -
12J LEU* 4.4 5.8 - - + -
15J PHE* 5.2 3.1 - - + -
61J SER 4.0 0.2 - - - +
62J THR* 3.2 2.8 - - - -
63J TYR* 2.8 74.6 + - + +
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Residues in contact with ILE 55 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24G VAL* 4.7 9.2 - - + -
26G PHE* 3.7 24.0 - - + -
32G MET* 3.7 24.2 - - + -
43G VAL* 3.1 7.9 - - - -
44G VAL* 2.9 42.6 + - + +
46G LEU* 3.9 27.8 - - + -
53G HIS* 3.9 7.6 - - + +
54G LEU* 1.3 75.6 - - - +
56G TYR* 1.3 75.2 + - - +
57G LYS 3.6 0.3 + - - -
59G ALA* 4.7 0.2 - - + -
60G ILE* 3.7 17.5 - - + -
61J SER 3.4 10.8 - - - +
62J THR* 3.9 12.6 - - - -
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Residues in contact with TYR 56 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42G TYR* 3.5 12.1 - - + +
43G VAL* 3.5 16.6 - - + -
54G LEU 5.6 0.2 - - - -
55G ILE* 1.3 78.2 - - - +
57G LYS* 1.3 65.8 + - - +
58G HIS* 3.3 33.7 - + + +
59G ALA* 2.9 19.1 + - - +
60G ILE 3.7 1.0 + - - -
79G ZN 4.6 3.1 - - - -
8J GLN* 2.5 40.5 + - + +
12J LEU* 4.4 0.7 - - - +
57J LYS* 3.5 22.0 - - + +
60J ILE* 3.7 33.4 - - + +
61J SER 3.0 11.6 + - - +
63J TYR* 2.9 44.7 + + - -
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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