Contacts of the strand formed by residues 85 - 94 (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 LEU 85 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81C ASP* 5.0 1.2 - - - +
72G GLN* 3.2 41.1 - - + +
73G ARG 3.7 9.4 - - - +
74G LYS* 3.6 31.4 - - + -
83G LEU* 3.2 17.3 - - + +
84G SER* 1.3 81.0 + - - +
86G VAL* 1.3 65.7 + - - +
87G THR* 4.2 4.8 + - + +
119G GLN* 4.1 15.3 - - - +
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Residues in contact with VAL 86 (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 4.0 4.9 - - - +
81C ASP* 3.7 11.0 - - - +
82C GLU* 3.6 32.1 - - + +
72G GLN* 3.3 1.6 - - - -
73G ARG* 2.7 45.8 + - + +
75G LYS* 3.6 34.1 - - + +
83G LEU* 4.2 7.4 - - + +
85G LEU* 1.3 80.3 - - - +
87G THR* 1.3 64.1 + - - +
88G LEU* 3.5 24.9 + - + -
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Residues in contact with THR 87 (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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80C GLY* 3.4 0.5 - - - -
81C ASP* 2.9 51.4 + - - +
70G LEU* 4.4 13.5 - - + +
71G ILE 3.8 5.1 + - - -
72G GLN* 3.7 30.5 - - - +
85G LEU* 4.8 4.0 - - + +
86G VAL* 1.3 74.2 - - - +
88G LEU* 1.3 60.1 + - - +
89G PHE 4.6 0.7 + - - -
90G ARG* 4.5 4.3 - - - +
134H ASP* 3.6 9.7 + - - +
15P ARG* 3.4 21.7 + - - +
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Residues in contact with LEU 88 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C PHE* 4.4 15.9 - - + -
80C GLY* 3.3 20.5 - - - +
54G ILE* 4.0 27.4 - - + -
71G ILE* 2.9 18.2 + - + +
73G ARG* 3.9 29.2 - - + +
86G VAL* 3.5 28.5 + - + +
87G THR* 1.3 71.0 - - - +
89G PHE* 1.3 86.2 + - + +
110G ALA* 4.1 18.2 - - + -
112G LEU* 4.8 1.6 - - + -
118G LEU* 4.2 7.4 - - + -
9H ILE* 5.9 0.2 - - - +
133H GLY 4.6 0.7 - - - +
134H ASP* 3.5 8.5 - - - +
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Residues in contact with PHE 89 (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* 6.1 1.1 - + - -
80C GLY 5.9 2.2 - - - -
54G ILE* 4.2 15.0 - - + -
69G HIS 4.1 0.2 - - - +
70G LEU* 3.5 0.5 - - - +
71G ILE* 2.8 53.0 + - + +
87G THR* 4.7 1.5 + - - -
88G LEU* 1.3 114.8 - - + +
90G ARG* 1.3 62.7 + - - +
106G SER* 3.9 18.8 - - - +
107G ALA 4.5 1.1 - - - -
108G GLY* 3.3 48.2 - - - -
109G ILE 3.6 15.5 - - - -
110G ALA* 4.6 0.2 - - + -
7H GLN* 4.5 9.9 - - - -
9H ILE* 6.4 1.6 - - + -
134H ASP* 3.5 6.1 - - - +
137H PHE* 4.0 25.6 - + + -
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Residues in contact with ARG 90 (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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69G HIS 3.2 5.2 - - - -
70G LEU* 3.3 35.4 - - + -
87G THR* 4.5 1.8 - - - +
89G PHE* 1.3 76.4 - - - +
91G CYS* 1.3 66.1 + - - +
92G ILE* 4.5 3.0 - - + +
106G SER* 4.8 2.2 - - - -
57H GLN* 3.2 19.9 + - - -
59H LEU* 4.3 10.9 - - - +
130H SER* 5.2 0.4 + - - -
132H ASP* 4.0 15.2 + - - -
134H ASP* 2.6 59.5 + - - +
135H VAL* 3.2 28.0 - - + +
12P LEU 5.4 0.4 - - - -
13P LEU* 2.9 28.2 + - + -
14P VAL* 3.8 17.2 + - - +
15P ARG* 3.2 27.1 - - - +
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Residues in contact with CYS 91 (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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68G GLY* 3.0 25.1 - - - -
69G HIS* 3.1 34.1 + - - +
90G ARG* 1.3 75.9 - - - +
92G ILE* 1.3 69.2 + - - +
104G CYS* 2.1 48.5 - - - -
106G SER* 4.0 18.4 - - - -
57H GLN* 4.4 2.9 - - - +
59H LEU* 6.4 0.2 - - - -
103H SER* 3.2 13.2 - - - +
135H VAL* 5.4 0.7 - - - -
13P LEU* 3.9 2.4 - - - +
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Residues in contact with ILE 92 (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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66G ALA* 4.1 11.4 - - + -
67G MET 3.2 12.1 - - - +
90G ARG* 4.5 7.2 - - + +
91G CYS* 1.3 84.5 - - - +
93G GLN* 1.3 70.6 + - - +
104G CYS* 4.9 1.0 - - - -
59H LEU* 4.2 26.5 - - + -
101H ASN* 3.3 29.8 - - + +
102H ASN* 3.5 0.7 - - - -
103H SER* 3.1 31.2 + - - +
135H VAL* 5.7 0.2 - - + -
13P LEU* 3.8 38.8 - - + +
14P VAL* 3.9 19.7 - - + -
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Residues in contact with GLN 93 (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* 5.3 2.9 - - + -
66G ALA* 3.4 0.3 - - - -
67G MET 2.8 36.4 + - - +
92G ILE* 1.3 85.4 - - - +
94G ASN* 1.3 62.5 + - - +
95G MET* 3.6 5.6 + - - +
102G ASN* 3.8 28.8 + - + +
103G SER 4.2 4.7 - - - +
104G CYS* 3.6 28.3 - - + -
93H GLN* 2.9 20.7 + - - +
101H ASN 3.8 2.2 - - - -
102H ASN* 3.5 4.0 + - - +
103H SER 3.6 9.4 - - - +
93I GLN* 2.7 41.6 + - - +
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Residues in contact with ASN 94 (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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65G TYR* 3.1 18.9 - - - +
66G ALA* 4.3 0.8 - - - +
93G GLN* 1.3 72.8 + - - +
95G MET* 1.3 62.1 + - - +
96G PRO* 4.4 0.2 - - - +
102G ASN* 3.0 21.0 + - - -
96H PRO* 3.1 36.9 - - + +
99H LEU 2.9 17.3 - - - +
101H ASN* 2.7 37.5 + - - +
102H ASN* 2.9 29.7 + - - +
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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