Contacts of the strand formed by residues 66 - 74 (chain G) in PDB entry 1OQE
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 66 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64G THR 2.6 10.7 + - - +
65G TYR* 1.3 105.7 - - + +
67G MET* 1.3 65.1 + - - +
92G ILE* 4.1 18.2 - - + -
93G GLN 3.4 5.8 - - - +
94G ASN* 4.4 4.5 - - - +
95G MET* 4.3 0.4 - - - +
124G ARG* 2.4 38.0 + - - +
101H ASN* 4.8 2.9 - - + -
13P LEU* 3.9 0.9 - - + -
14P VAL* 5.0 2.9 - - + -
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Residues in contact with MET 67 (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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60G TYR* 3.5 39.5 - - + -
62G ASP* 3.6 33.9 - - + +
64G THR* 3.8 17.3 - - - -
66G ALA* 1.3 80.9 - - - +
68G GLY* 1.3 59.7 + - - +
92G ILE* 3.2 4.9 - - - +
93G GLN* 2.8 32.3 + - - +
95G MET* 3.6 24.2 - - + -
122G ILE* 4.4 1.1 - - + -
124G ARG* 3.6 31.2 - - + +
127G ALA* 3.8 15.9 - - + -
129G ILE* 4.3 0.2 - - + -
13P LEU* 3.3 7.6 - - - -
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Residues in contact with GLY 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60G TYR* 2.9 25.3 + - - -
67G MET* 1.3 79.6 - - - +
69G HIS* 1.3 58.3 + - - -
91G CYS* 3.0 16.4 - - - -
92G ILE* 4.3 0.2 - - - -
93G GLN 5.0 0.2 - - - -
104G CYS* 5.7 0.4 - - - -
122G ILE* 3.4 19.9 - - - +
123G PRO* 3.4 8.1 - - - +
124G ARG* 5.6 0.4 - - - +
13P LEU* 3.4 11.6 - - - +
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Residues in contact with HIS 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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56G GLY* 3.6 20.4 + - - -
58G VAL* 3.6 15.1 - - + +
60G TYR* 2.6 27.9 + + - +
68G GLY* 1.3 72.4 - - - +
70G LEU* 1.3 66.1 + - - +
71G ILE* 4.7 8.0 - - + +
90G ARG* 3.2 5.2 - - - +
91G CYS* 3.1 43.5 + - - +
104G CYS 3.1 26.5 - - - -
106G SER* 5.0 4.5 + - - -
120G LEU* 3.4 39.7 - - + +
121G ALA 3.2 13.0 - - - +
122G ILE* 4.0 3.1 - - + -
123G PRO* 4.4 1.3 - - - -
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Residues in contact with LEU 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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22G TYR* 4.4 15.3 - - + +
69G HIS* 1.3 79.6 - - - +
71G ILE* 1.3 63.4 + - - +
72G GLN* 3.6 32.8 + - + +
87G THR* 4.4 11.7 - - + +
89G PHE 3.5 5.4 - - - +
90G ARG* 3.3 37.9 - - + -
119G GLN 3.5 1.0 - - - +
120G LEU* 3.3 5.4 - - - +
121G ALA* 2.7 42.0 + - + +
123G PRO* 3.9 24.9 - - + -
12P LEU* 5.5 4.7 - - + +
13P LEU* 4.4 5.6 - - + -
15P ARG* 5.1 3.6 - - - +
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Residues in contact with ILE 71 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54G ILE* 3.6 26.5 - - + -
55G TYR* 3.9 11.2 - - - +
56G GLY* 3.8 28.3 - - - +
69G HIS* 4.7 5.2 - - + -
70G LEU* 1.3 75.0 - - - +
72G GLN* 1.3 62.3 + - - +
87G THR* 3.7 1.6 - - - -
88G LEU* 2.9 32.6 + - + +
89G PHE* 2.8 38.5 + - + +
106G SER* 4.0 12.6 - - - +
118G LEU* 5.1 1.6 - - + -
119G GLN 3.5 4.3 - - - +
120G LEU* 4.0 17.3 - - + -
138G PHE* 4.1 11.0 - - + -
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Residues in contact with GLN 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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22G TYR* 5.4 6.4 + - - -
24G PHE* 5.6 0.2 - - - -
70G LEU* 3.6 35.0 - - + +
71G ILE* 1.3 79.4 - - - +
73G ARG* 1.3 60.5 - - - +
85G LEU* 3.2 30.8 - - + +
86G VAL 3.3 7.9 - - - +
87G THR* 3.7 18.5 - - - +
88G LEU* 4.7 1.3 - - - -
117G GLU 3.7 0.3 - - - +
118G LEU* 3.2 12.1 - - - +
119G GLN* 2.8 64.2 + - + +
121G ALA* 3.9 12.1 - - - +
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Residues in contact with ARG 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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79C PHE* 5.7 6.7 - - - +
82C GLU* 4.3 7.1 + - - -
72G GLN* 1.3 75.5 - - - +
74G LYS* 1.3 68.7 + - - +
75G LYS* 3.6 37.3 + - - +
84G SER 3.3 4.0 - - - +
85G LEU* 3.4 3.0 - - - -
86G VAL* 2.7 45.3 + - + +
88G LEU* 3.9 24.6 - - + +
111G LYS* 3.6 18.4 + - - +
112G LEU* 3.7 21.1 - - + +
113G GLU* 3.9 18.2 - - - +
116G ASP* 2.8 33.8 + - + +
117G GLU 3.5 6.3 - - - +
118G LEU* 4.2 2.0 - - + -
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Residues in contact with LYS 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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43G LYS* 3.2 25.8 - - + +
72G GLN 4.3 0.2 - - - -
73G ARG* 1.3 71.6 - - - +
75G LYS* 1.3 65.8 + - - +
84G SER 3.4 6.1 - - - +
85G LEU* 3.6 19.1 - - + -
115G GLY 4.4 1.2 - - - +
116G ASP* 3.3 7.7 - - - -
117G GLU* 2.8 55.2 + - + +
119G GLN* 3.5 32.3 - - + +
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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