Contacts of the strand formed by residues 50 - 56 (chain G) in PDB entry 4GG6
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 PRO 50 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42G TYR* 4.7 12.1 - - + -
43G ARG 3.1 13.5 - - - +
44G GLN* 3.7 24.4 - - + +
49G GLY* 1.3 87.9 - - - +
51G GLU* 1.3 63.0 + - - +
103G TYR* 4.9 7.9 - - + -
118G PHE* 5.3 13.5 - - + -
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Residues in contact with GLU 51 (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* 3.4 8.7 - - - -
43G ARG* 2.8 83.2 + - + +
44G GLN* 5.7 0.4 - - - -
45G LEU* 5.9 3.8 - - + +
48G GLN* 4.8 9.6 - - - +
49G GLY 4.7 5.1 - - - +
50G PRO* 1.3 77.5 - - - +
52G TYR* 1.3 69.6 + - - +
75G MET* 5.3 6.2 - - - +
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Residues in contact with TYR 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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40G HIS* 4.7 4.0 - + - -
42G TYR* 3.4 45.0 - + + +
51G GLU* 1.3 78.8 - - - +
53G VAL* 1.3 74.5 + - - +
54G ILE* 3.3 24.6 - - - +
55G HIS* 2.6 47.1 + + + -
68G ASN* 3.9 10.5 + - - -
75G MET* 3.4 32.3 - - + +
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Residues in contact with VAL 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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41G TRP* 2.8 27.0 + - + +
42G TYR 3.9 2.0 - - - -
43G ARG* 3.7 39.9 - - + +
51G GLU 3.9 1.1 - - - +
52G TYR* 1.3 82.5 - - - +
54G ILE* 1.3 52.7 + - - +
68G ASN* 2.7 31.5 + - - +
75G MET* 3.9 17.3 - - + +
76G ALA* 3.7 27.8 - - + -
89G LEU* 4.1 14.4 - - + -
91G LEU* 4.9 4.9 - - + -
102G TYR* 4.6 6.3 - - + -
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Residues in contact with ILE 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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39G ILE 4.2 0.2 - - - +
40G HIS* 3.7 0.2 - - - -
41G TRP* 2.9 30.5 + - + -
52G TYR* 3.3 16.5 - - - +
53G VAL* 1.3 80.7 - - + +
55G HIS* 1.3 71.7 + - - +
66G VAL* 3.4 32.8 - - + +
67G ASN* 3.9 0.4 - - - +
68G ASN* 3.3 17.3 - - - +
76G ALA 3.4 28.3 - - - +
78G LEU* 3.8 27.4 - - + +
89G LEU* 3.5 28.7 - - + -
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Residues in contact with HIS 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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66B GLU* 5.2 21.5 + - + +
70B ARG* 6.3 1.2 - - - +
38G TYR* 3.6 31.0 - + - -
39G ILE 3.0 13.9 - - - +
40G HIS* 3.5 31.6 - + + +
52G TYR* 2.6 37.0 + + + -
54G ILE* 1.3 77.4 - - - +
56G GLY* 1.3 57.8 + - - +
66G VAL* 3.7 19.6 - - - +
78G LEU* 3.9 6.5 - - - -
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Residues in contact with GLY 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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38G TYR* 3.3 14.7 - - - -
39G ILE* 2.8 39.3 + - - +
55G HIS* 1.3 76.9 - - - +
57G LEU* 1.3 59.7 + - - -
66G VAL* 3.9 17.0 - - - -
78G LEU* 3.7 7.6 - - - +
80G ILE* 4.0 5.6 - - - -
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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