Contacts of the strand formed by residues 87 - 96 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85K ALA* 3.1 16.5 + - + +
86K LYS* 1.3 70.7 - - - +
88K LEU* 1.3 72.2 + - - +
89K HIS* 3.9 1.6 + - - +
144K LEU* 3.7 30.8 - - + +
145K PHE 3.8 4.9 - - - +
146K LEU* 3.5 22.2 - - + -
195K ASN* 5.0 13.1 + - - +
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Residues in contact with LEU 88 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86K LYS* 4.1 13.9 - - + +
87K VAL* 1.3 76.5 - - - +
89K HIS* 1.3 62.1 + - - +
90K GLY 4.0 0.2 - - - -
144K LEU* 3.6 8.3 - - - +
145K PHE* 3.0 55.9 + - + +
147K VAL* 4.2 24.5 - - + -
197K LEU* 5.2 14.8 - - + -
209K PHE* 6.1 5.4 - - + -
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Residues in contact with HIS 89 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87K VAL 3.9 1.3 + - - +
88K LEU* 1.3 75.4 - - - +
90K GLY* 1.3 61.1 + - - +
91K GLU 3.2 19.5 + - - -
92K GLN* 3.1 19.2 + - - -
142K PHE* 4.2 10.7 - + - -
143K SER 3.6 7.5 + - - -
144K LEU* 4.4 11.7 - - + -
193K ASP* 5.9 0.8 + - - -
216K GLY* 5.5 5.4 + - - +
217K LEU* 3.3 49.4 + - + +
246K PHE* 3.2 31.5 - + + +
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Residues in contact with GLY 90 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88K LEU 4.0 2.4 + - - -
89K HIS* 1.3 73.2 - - - +
91K GLU* 1.3 65.9 + - - +
143K SER* 2.9 19.1 + - - -
144K LEU* 4.5 3.5 - - - +
145K PHE* 5.3 4.2 - - - +
245K ARG* 4.1 1.2 - - - +
246K PHE* 2.8 34.9 + - - +
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Residues in contact with GLU 91 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89K HIS* 3.2 12.1 + - - -
90K GLY* 1.3 82.4 - - - +
92K GLN* 1.3 62.5 + - - +
141K GLN 4.7 0.2 - - - -
143K SER* 3.1 42.3 + - - +
161K VAL* 4.5 10.0 - - - +
162K LYS 4.9 0.2 - - - +
164K ALA* 4.2 2.7 + - - +
243K LYS* 3.0 26.9 + - - +
244K ALA 3.3 14.4 - - - +
245K ARG* 2.7 45.8 + - + +
246K PHE* 3.8 5.4 - - - -
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Residues in contact with GLN 92 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62K VAL* 3.7 13.2 - - + +
89K HIS* 3.1 19.1 + - - -
91K GLU* 1.3 76.4 - - - +
93K TYR* 1.3 81.6 + - - +
140K ASN* 3.5 19.2 + - - +
141K GLN 3.8 7.3 + - - -
142K PHE* 3.3 23.9 - - - -
217K LEU* 3.6 20.0 - - + -
220K PHE* 3.9 21.6 - - + -
242K VAL 4.0 0.2 - - - +
243K LYS* 3.5 5.1 - - - +
244K ALA* 3.0 30.9 + - - +
246K PHE* 3.9 20.6 - - + -
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Residues in contact with TYR 93 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92K GLN* 1.3 84.9 + - - +
94K LEU* 1.3 60.9 + - - +
95K GLU* 2.8 46.9 + - + +
139K HIS* 4.1 17.0 - + - -
140K ASN* 3.4 4.7 - - - -
141K GLN* 2.9 48.3 + - + +
162K LYS* 3.6 48.7 + - + -
241K ALA* 3.8 13.0 - - + +
242K VAL* 3.3 17.5 - - - -
243K LYS* 3.9 20.2 - - + +
285K TYR* 4.0 15.9 - - - -
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Residues in contact with LEU 94 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58K PRO 3.3 27.4 - - - +
59K THR* 3.5 21.1 - - + -
61K GLY* 4.1 4.9 - - - -
62K VAL* 3.7 20.0 - - + +
93K TYR* 1.3 78.1 - - - +
95K GLU* 1.3 73.2 + - - +
96K LEU* 4.1 17.3 - - + -
138K CYS* 4.3 3.8 - - + -
139K HIS 3.4 9.9 - - - +
140K ASN* 3.3 27.4 - - - +
220K PHE* 5.1 0.4 - - + -
239K PHE* 5.6 2.2 - - + -
241K ALA* 3.1 4.3 - - - +
242K VAL* 2.8 44.2 + - + +
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Residues in contact with GLU 95 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93K TYR* 2.8 29.1 + - + +
94K LEU* 1.3 75.8 - - - +
96K LEU* 1.3 66.3 + - - +
97K TYR* 3.5 43.7 + - + -
138K CYS* 3.3 6.6 - - - +
139K HIS* 3.0 35.2 + - + +
162K LYS* 4.6 7.4 + - - -
240K LYS* 3.3 13.2 - - + +
241K ALA* 3.8 7.9 - - + -
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Residues in contact with LEU 96 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58K PRO* 3.3 52.5 - - + +
94K LEU* 4.1 13.0 - - + -
95K GLU* 1.3 74.4 - - - +
97K TYR* 1.3 65.5 + - - +
98K LYS* 3.1 12.4 + - - +
99K PRO* 5.4 2.0 - - + -
100K LEU* 4.0 21.8 - - + +
137K ILE 3.9 2.5 - - - -
138K CYS* 4.0 19.7 - - + -
236K VAL* 5.3 2.7 - - + +
239K PHE* 3.5 28.8 - - + +
240K LYS* 2.7 23.1 + - - +
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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