Contacts of the strand formed by residues 68 - 79 (chain G) in PDB entry 6A5T
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 68 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1448A ILE* 4.6 3.4 - - + -
11G LEU 3.2 1.4 - - - +
12G THR* 2.9 10.9 - - - -
13G LEU* 2.9 44.0 + - + +
18G PHE* 4.3 9.2 - - + -
60G ARG 3.2 8.3 - - - +
61G ILE* 3.9 17.3 - - + +
62G ILE* 3.8 4.5 - - - -
67G SER* 1.3 74.4 - - - +
69G GLU* 1.3 60.0 + - - +
70G PHE* 4.0 17.4 + - + -
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Residues in contact with GLU 69 (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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11A LEU 5.7 1.2 - - - +
12A ARG* 5.9 3.3 + - - +
10G ILE* 3.8 33.4 - - + +
11G LEU 3.2 4.5 - - - +
12G THR* 5.7 0.4 - - - +
59G GLY* 3.5 1.4 - - - -
60G ARG* 2.4 89.8 + - + +
62G ILE* 3.6 18.9 - - + +
68G ALA* 1.3 67.5 - - - +
70G PHE* 1.3 67.4 + - - +
71G GLU* 4.2 2.5 + - + +
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Residues in contact with PHE 70 (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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1448A ILE* 3.9 18.2 - - + -
9G LEU 3.3 1.7 - - - +
10G ILE* 3.2 9.2 - - - +
11G LEU* 2.9 56.3 + - + +
13G LEU* 3.6 25.6 - - + -
22G MET* 5.1 7.2 - - + -
26G LEU* 3.4 48.7 - - + -
56G VAL* 5.0 17.5 - - + -
57G GLY 5.6 0.2 - - - -
59G GLY* 3.3 35.0 - - - -
68G ALA* 4.6 4.7 - - + -
69G GLU* 1.3 77.4 - - - +
71G GLU* 1.3 60.1 + - - +
72G VAL* 3.6 11.3 + - + -
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Residues in contact with GLU 71 (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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8G SER* 4.6 15.9 + - - -
9G LEU 3.4 4.5 - - - +
10G ILE* 3.8 20.6 - - + -
56G VAL* 3.2 23.2 + - - +
58G LYS 5.9 1.2 + - - -
69G GLU* 4.2 3.2 + - + +
70G PHE* 1.3 70.0 - - - +
72G VAL* 1.3 62.1 + - - +
73G LYS* 3.2 32.0 + - + +
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Residues in contact with VAL 72 (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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7G LEU 3.8 0.2 - - - +
8G SER* 3.1 5.7 - - - -
9G LEU* 2.8 44.2 + - + +
11G LEU* 4.2 25.8 - - + -
26G LEU* 6.1 1.6 - - + +
30G LEU* 3.5 37.5 - - + -
54G ILE* 4.7 6.1 - - + -
55G ASP 4.9 1.3 - - - +
56G VAL* 4.3 22.4 - - + +
70G PHE* 4.6 8.5 - - + +
71G GLU* 1.3 69.1 - - - +
73G LYS* 1.3 65.9 + - - +
74G TYR* 3.7 13.2 - - + -
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Residues in contact with LYS 73 (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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41D HIS* 3.3 58.3 - - + +
7G LEU 3.5 4.7 - - - +
8G SER* 4.5 2.9 - - - +
54G ILE* 4.2 3.5 - - - +
55G ASP 3.5 20.1 + - - +
56G VAL 5.2 2.1 + - - +
71G GLU* 3.2 34.7 + - + +
72G VAL* 1.3 75.5 - - - +
74G TYR* 1.3 65.1 + - - +
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Residues in contact with TYR 74 (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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41D HIS* 3.6 8.7 + - - -
6G ASP* 3.5 3.8 - - - -
7G LEU* 2.8 72.7 + - + +
8G SER 5.0 0.2 - - - -
9G LEU* 4.4 11.7 - - + +
30G LEU* 4.2 16.4 - - + -
34G VAL* 3.5 30.7 - - + +
45G ILE* 3.8 5.9 - - - +
48G VAL* 5.3 11.0 - - + -
54G ILE* 4.6 15.0 - - + -
72G VAL* 3.7 30.1 - - + -
73G LYS* 1.3 76.6 - - - +
75G ARG* 1.3 74.2 + - - +
76G ALA* 3.5 20.0 - - + -
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Residues in contact with ARG 75 (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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40D ASP* 4.6 13.5 - - - +
41D HIS* 4.9 8.8 - - + -
46D HIS* 4.5 18.6 + - - -
49D ILE* 5.4 4.7 - - - -
4G LEU* 4.4 27.7 - - + +
5G LYS 3.1 13.0 - - - +
6G ASP* 2.3 44.4 + - - +
48G VAL* 5.0 1.2 - - - +
49G LEU* 4.1 25.5 + - + +
74G TYR* 1.3 82.7 - - - +
76G ALA* 1.3 61.7 + - - +
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Residues in contact with ALA 76 (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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4G LEU* 3.4 6.3 - - - -
5G LYS* 2.9 31.5 + - - +
7G LEU* 4.3 7.4 - - + +
45G ILE* 4.6 8.7 - - + -
47G THR 3.2 17.3 - - - +
48G VAL* 4.4 6.3 - - + +
49G LEU 4.9 0.4 - - - +
74G TYR* 3.5 27.7 - - + -
75G ARG* 1.3 74.2 - - - +
77G VAL* 1.3 66.7 + - - +
78G VAL* 3.7 4.8 + - + +
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Residues in contact with VAL 77 (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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51D LEU* 4.9 7.0 - - + -
56D SER* 5.3 2.5 - - - -
59D LEU* 5.7 4.3 - - + -
60D ILE* 4.3 21.5 - - + -
2G PHE* 4.2 22.4 - - + -
3G PHE 3.4 11.9 - - - +
4G LEU* 3.4 19.7 - - + -
45G ILE* 3.7 0.7 - - - -
46G VAL* 2.7 35.3 + - + +
47G THR* 2.9 29.7 + - - +
49G LEU* 4.5 16.2 - - + -
76G ALA* 1.3 72.9 - - - +
78G VAL* 1.3 59.4 + - - +
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Residues in contact with VAL 78 (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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34D PHE* 6.3 2.5 - - + -
1G MET 3.8 0.2 - - - +
2G PHE* 3.4 7.2 - - - -
3G PHE* 2.8 62.7 + - + +
5G LYS* 4.3 17.7 - - + -
7G LEU* 5.1 4.7 - - + -
42G PHE* 3.3 40.2 - - + +
44G TYR 3.2 11.4 - - - +
45G ILE* 4.4 10.1 - - + -
46G VAL* 3.7 2.9 - - - -
76G ALA* 4.1 8.1 - - + +
77G VAL* 1.3 79.5 - - - +
79G TRP* 1.3 59.1 + - - +
80G LYS* 5.6 0.7 - - + +
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Residues in contact with TRP 79 (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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105D THR* 5.1 2.9 - - + -
108D TYR* 4.1 14.9 - + - -
1G MET 2.9 39.7 - - - +
2G PHE* 3.2 37.1 - + + -
43G GLY* 3.4 0.2 - - - -
44G TYR* 2.8 65.0 + + + -
46G VAL* 3.3 15.5 - - + +
78G VAL* 1.3 73.0 - - - +
80G LYS* 1.3 61.4 + - - +
81G PRO* 3.4 36.1 - - + -
85G GLU* 5.4 1.8 - - - -
87G VAL* 6.2 1.1 - - + -
103G VAL* 4.3 8.5 - - + -
104G GLY* 3.5 15.9 - - - -
105G PRO* 3.3 37.2 - - + +
106G LEU* 4.7 6.7 - - + -
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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