Contacts of the strand formed by residues 87 - 96 (chain G) in PDB entry 1S9C
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 VAL 87 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74G LEU* 4.7 5.6 - - + -
82G ILE* 3.7 9.2 - - + -
83G ASN 3.3 18.6 - - - +
84G PHE* 3.4 35.4 + - + +
85G ALA 3.4 2.5 + - - +
86G LYS* 1.3 77.1 - - - +
88G LEU* 1.3 73.8 + - - +
144G LEU* 4.3 21.5 - - + -
145G PHE 3.4 4.3 - - - +
146G LEU* 3.4 29.8 - - + -
195G ASN* 4.9 8.7 + - - -
197G LEU* 5.9 1.4 - - - +
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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
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85G ALA 6.2 0.2 - - - +
86G LYS* 5.2 0.9 - - - -
87G VAL* 1.3 83.4 - - - +
89G HIS* 1.3 60.2 + - - +
90G GLY* 3.8 0.4 - - - -
144G LEU* 3.4 7.2 - - - +
145G PHE* 2.6 54.7 + - + +
147G VAL* 3.3 33.7 - - + -
197G LEU* 4.8 11.4 - - + -
209G PHE* 4.4 27.4 - - + -
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Residues in contact with HIS 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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69G MET* 4.0 17.5 - - + +
88G LEU* 1.3 74.7 - - - +
90G GLY* 1.3 57.5 + - - +
91G GLU 2.9 28.6 + - - -
92G GLN* 3.1 21.4 + - - -
142G PHE* 4.1 8.1 - + - -
143G SER 3.6 5.8 - - - -
144G LEU* 4.3 15.0 - - + -
216G GLY* 5.7 2.1 - - - -
217G LEU* 3.4 39.2 + - + +
246G PHE* 3.2 33.3 - + + +
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Residues in contact with GLY 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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88G LEU 3.7 3.6 + - - -
89G HIS* 1.3 73.1 - - - +
91G GLU* 1.3 65.3 + - - +
143G SER* 2.7 17.7 + - - -
144G LEU* 4.3 1.0 - - - +
145G PHE* 4.5 8.3 - - - +
245G ARG* 4.2 0.5 - - - +
246G PHE* 2.8 35.0 + - - +
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Residues in contact with GLU 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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89G HIS* 2.9 17.9 + - - -
90G GLY* 1.3 82.0 - - - +
92G GLN* 1.3 62.7 + - - +
141G GLN 4.6 0.2 - - - -
143G SER* 3.0 40.2 + - - +
161G VAL* 4.6 10.2 - - - +
164G ALA* 4.4 1.3 + - - +
243G LYS* 3.3 23.4 + - - +
244G ALA 3.4 11.4 - - - +
245G ARG* 2.5 51.7 + - + +
246G PHE* 3.7 4.2 - - - -
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Residues in contact with GLN 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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62G VAL* 3.7 9.8 - - + +
89G HIS* 3.1 15.5 + - - +
91G GLU* 1.3 75.2 - - - +
93G TYR* 1.3 75.4 + - - +
140G ASN* 3.1 28.3 + - - +
141G GLN 3.7 4.9 - - - +
142G PHE* 2.9 41.2 - - - -
217G LEU* 3.5 17.9 - - + -
220G PHE* 4.0 20.2 - - + -
242G VAL 4.2 0.2 - - - +
243G LYS* 3.5 3.8 - - - +
244G ALA* 3.0 32.4 + - - +
246G PHE* 3.8 15.0 - - + -
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Residues in contact with TYR 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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92G GLN* 1.3 83.8 + - - +
94G LEU* 1.3 62.8 + - - +
95G GLU* 2.8 46.4 + - + +
139G HIS* 4.0 15.7 - - - -
140G ASN* 3.1 5.4 - - - -
141G GLN* 2.7 50.9 + - + +
162G LYS* 3.5 51.1 + - + +
241G ALA* 4.0 8.8 - - + +
242G VAL 3.4 17.5 - - - -
243G LYS* 3.8 21.1 - - + +
285G TYR* 3.9 17.3 - - - -
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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 PRO 3.4 26.5 - - - +
59G THR* 3.7 9.4 - - + -
61G GLY* 4.0 3.6 - - - -
62G VAL* 3.6 31.0 - - + +
93G TYR* 1.3 79.3 - - - +
95G GLU* 1.3 72.4 + - - +
96G LEU* 4.1 10.8 - - + -
138G CYS* 3.9 13.2 - - + -
139G HIS 3.2 8.7 - - - +
140G ASN* 3.3 27.6 - - - +
220G PHE* 5.1 0.7 - - + -
239G PHE* 5.9 1.3 - - + -
241G ALA* 3.2 3.6 - - - +
242G VAL* 2.8 47.4 + - + +
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Residues in contact with GLU 95 (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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93G TYR* 2.8 28.5 + - + +
94G LEU* 1.3 76.8 - - - +
96G LEU* 1.3 66.8 + - - +
97G TYR* 3.6 43.7 + - + -
138G CYS* 3.1 6.4 - - - +
139G HIS* 2.8 34.4 + - + +
162G LYS* 4.3 10.6 + - - -
240G LYS* 3.5 11.9 - - + +
241G ALA* 3.6 9.6 - - + -
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Residues in contact with LEU 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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58G PRO* 3.5 47.1 - - + +
94G LEU* 4.1 12.3 - - + -
95G GLU* 1.3 75.3 - - - +
97G TYR* 1.3 65.2 + - - +
98G LYS* 3.1 11.9 + - - +
99G PRO* 5.2 2.5 - - + -
100G LEU* 4.0 22.7 - - + +
137G ILE 3.6 2.7 - - - +
138G CYS* 3.6 22.4 - - + -
236G VAL* 5.6 1.1 - - + +
239G PHE* 3.5 28.6 - - + +
240G LYS* 2.7 26.2 + - - +
241G ALA* 5.7 0.2 - - - -
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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