Contacts of the strand formed by residues 87 - 98 (chain G) in PDB entry 3IT8
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 TYR 87 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84G ALA* 3.1 18.9 + - + +
85G VAL 3.3 0.8 - - - -
86G SER* 1.3 80.9 - - - +
88G GLN* 1.3 54.9 + - - +
89G THR* 2.6 44.5 + - - +
91G VAL* 4.3 4.7 - - + -
58K HIS* 2.6 46.5 + + - +
153K ALA 5.5 1.1 - - - -
157K GLY* 3.5 26.5 - - - +
158K PHE* 4.8 2.0 - + - -
160K TYR* 4.3 11.7 - - + -
161K MET* 4.2 18.8 - - + -
162K GLY* 3.5 25.5 - - - -
165K LEU* 4.1 8.1 - - + -
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Residues in contact with GLN 88 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83G ILE* 3.4 24.5 - - + -
84G ALA 3.2 5.6 + - - -
85G VAL* 3.0 33.3 + - - +
86G SER 4.4 0.6 - - - -
87G TYR* 1.3 65.2 - - - +
89G THR* 1.3 65.8 + - - +
153K ALA* 6.3 0.6 - - - +
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Residues in contact with THR 89 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82G ARG 3.1 12.7 - - - +
83G ILE* 3.7 9.5 - - - +
84G ALA 4.6 0.3 + - - -
87G TYR* 2.6 38.7 + - - +
88G GLN* 1.3 79.7 + - - +
90G LYS* 1.3 76.9 + - + +
91G VAL* 3.2 8.7 + - - +
58K HIS* 4.7 13.5 - - + -
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Residues in contact with LYS 90 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47G GLN* 4.0 17.0 - - - +
81G SER* 3.9 21.1 - - - +
82G ARG 3.6 6.1 - - - -
83G ILE* 4.2 12.7 - - + +
89G THR* 1.3 83.2 - - + +
91G VAL* 1.3 62.1 + - - +
92G ASN* 5.2 2.6 - - - +
133G SER* 4.0 9.0 - - - -
135G GLU* 3.1 39.2 + - - +
58K HIS* 5.3 1.9 - - - -
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Residues in contact with VAL 91 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81G SER* 3.5 1.0 - - - -
82G ARG* 3.0 49.0 + - + +
84G ALA* 5.8 1.1 - - + +
87G TYR* 4.3 10.5 - - + -
89G THR 3.6 8.7 - - - +
90G LYS* 1.3 78.6 - - - +
92G ASN* 1.3 66.3 + - - +
93G LEU* 3.5 0.6 + - + -
34H ASN* 3.8 23.6 - - - +
58K HIS* 4.6 5.8 - - + +
161K MET* 4.2 13.2 - - - -
165K LEU* 3.8 30.7 - - + -
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Residues in contact with ASN 92 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79G THR* 3.6 18.5 + - - +
80G ILE 3.9 3.8 - - - +
81G SER* 3.2 18.2 + - - -
90G LYS* 5.2 2.3 - - - +
91G VAL* 1.3 75.0 + - - +
93G LEU* 1.3 63.7 + - - +
94G LEU 4.8 4.3 - - - +
95G SER* 4.7 4.0 + - - -
34H ASN* 4.9 2.9 + - - +
146H GLU* 2.5 39.6 + - - +
147H SER* 4.0 15.3 + - - -
148H GLY* 4.4 3.3 + - - +
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Residues in contact with LEU 93 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58G ILE* 4.0 27.1 - - + -
80G ILE* 2.8 18.3 + - + +
81G SER 4.7 1.1 - - - -
82G ARG* 3.7 36.1 - - + +
91G VAL 4.3 1.1 - - - +
92G ASN* 1.3 77.2 - - - +
94G LEU* 1.3 74.9 + - + +
124G PHE* 3.7 33.3 - - + -
126G LEU* 5.0 0.2 - - + -
132G LEU* 4.1 6.3 - - + -
15H HIS* 4.9 2.6 + - - -
34H ASN* 3.5 43.3 - - + +
148H GLY* 3.4 15.9 - - - -
151H TYR* 5.0 0.3 - - - -
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Residues in contact with LEU 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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58G ILE* 4.0 6.7 - - + +
79G THR* 3.3 1.4 + - - -
80G ILE* 2.8 53.6 + - + +
92G ASN* 4.9 0.2 - - - +
93G LEU* 1.3 88.7 + - + +
95G SER* 1.3 64.5 + - - +
120G LEU* 3.7 16.6 - - + -
121G GLY* 3.6 28.5 - - - +
122G GLY 3.7 5.6 - - - +
124G PHE* 3.6 24.2 - - + -
148H GLY* 3.4 5.8 - - - +
151H TYR* 3.4 38.8 - - + +
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Residues in contact with SER 95 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77G THR* 5.5 1.2 - - - -
78G HIS 3.3 10.8 + - - -
79G THR* 3.6 16.0 - - - +
92G ASN* 4.7 2.7 + - - -
94G LEU* 1.3 77.5 - - - +
96G ALA* 1.3 66.7 + - - +
97G ILE* 5.1 1.9 - - - +
120G LEU* 4.0 6.0 - - - +
61H GLN* 3.3 11.8 + - - +
63H LEU* 5.0 0.2 - - - +
146H GLU* 3.8 30.6 + - - +
148H GLY* 2.7 18.0 + - - +
149H GLN* 3.3 18.8 + - - +
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Residues in contact with ALA 96 (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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77G THR* 3.4 4.3 - - - -
78G HIS 3.0 29.2 + - - +
95G SER* 1.3 78.2 + - - +
97G ILE* 1.3 68.4 + - - +
118G ILE* 3.8 19.9 - - + +
120G LEU* 3.7 19.5 - - + +
61H GLN* 4.1 4.7 - - - +
63H LEU* 4.6 6.3 - - - -
117H PRO* 4.0 21.1 - - + -
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Residues in contact with ILE 97 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75G LEU* 4.4 15.5 - - + -
76G LEU 3.3 11.2 - - - +
77G THR* 4.2 18.4 - - + -
95G SER* 5.1 2.0 - - - +
96G ALA* 1.3 81.5 - - - +
98G LYS* 1.3 65.2 + - - +
118G ILE* 4.7 1.6 - - - -
63H LEU* 4.2 8.4 - - + +
115H TYR* 3.5 57.4 - - + +
117H PRO* 3.2 22.1 - - - +
143H LEU* 4.5 1.3 - - + -
149H GLN* 3.6 25.8 - - - +
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Residues in contact with LYS 98 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75G LEU* 3.9 0.9 - - - -
76G LEU* 2.8 37.7 + - + +
97G ILE* 1.3 79.6 - - - +
99G SER* 1.3 63.2 + - - +
100G PRO* 3.3 5.2 - - - +
116G GLU* 3.1 43.1 + - + +
117G PRO* 2.9 28.2 + - - +
118G ILE* 4.0 19.5 - - + -
98H LYS* 3.5 21.1 - - - +
115H TYR* 3.9 4.0 - - - +
116H GLU* 3.7 11.9 - - - +
117H PRO* 4.2 13.0 - - + +
98I LYS* 3.4 26.8 - - - +
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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