Contacts of the strand formed by residues 88 - 96 (chain J) 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 LEU 88 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86J LYS 3.7 8.7 + - - +
87J VAL* 1.3 82.2 - - - +
89J HIS* 1.3 60.9 + - - +
90J GLY 3.5 2.3 + - - -
144J LEU* 3.2 6.9 - - - -
145J PHE* 2.8 70.7 + - + +
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Residues in contact with HIS 89 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69J MET* 5.2 6.9 - - + +
87J VAL 3.9 3.2 + - - +
88J LEU* 1.3 70.2 - - - +
90J GLY* 1.3 60.8 + - - +
91J GLU 2.7 35.2 + - - -
92J GLN* 2.8 28.8 + - + +
142J PHE* 3.6 17.7 - + - -
143J SER 3.9 5.8 - - - -
144J LEU* 4.2 13.0 - - + +
217J LEU* 4.1 25.5 - - + +
246J PHE* 3.5 24.4 - + + +
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Residues in contact with GLY 90 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88J LEU 3.5 3.8 + - - -
89J HIS* 1.3 74.3 - - - +
91J GLU* 1.3 66.6 + - - +
143J SER* 2.9 16.5 + - - -
144J LEU 5.0 0.8 - - - -
145J PHE* 5.6 2.7 - - - +
245J ARG* 3.8 3.6 - - - +
246J PHE* 3.1 31.0 + - - +
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Residues in contact with GLU 91 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89J HIS* 2.7 25.2 + - - -
90J GLY* 1.3 83.1 - - - +
92J GLN* 1.3 57.4 + - - +
143J SER* 3.2 38.4 + - - +
162J LYS 4.4 2.1 - - - +
163J VAL* 5.5 0.7 - - - -
164J ALA* 3.9 5.4 + - - +
243J LYS* 3.1 28.8 + - - +
244J ALA 3.3 11.7 - - - +
245J ARG* 2.9 44.3 + - + +
246J PHE* 4.4 2.7 - - - -
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Residues in contact with GLN 92 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62J VAL* 3.9 11.3 - - + +
89J HIS* 2.8 31.5 + - + +
91J GLU* 1.3 76.0 - - - +
93J TYR* 1.3 73.2 + - - +
140J ASN* 3.2 28.1 + - - +
141J GLN 3.8 4.9 - - - +
142J PHE* 3.0 27.5 - - - -
217J LEU* 4.0 13.5 - - + -
220J PHE* 4.1 20.5 - - + -
242J VAL 4.0 0.4 - - - +
243J LYS* 3.2 8.6 - - - +
244J ALA 3.0 30.3 + - - +
246J PHE* 4.2 13.5 - - + -
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Residues in contact with TYR 93 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92J GLN* 1.3 82.3 + - - +
94J LEU* 1.3 62.0 + - - +
95J GLU* 2.9 46.0 + - + +
139J HIS* 4.0 13.0 - - - -
140J ASN* 3.2 6.4 - - - -
141J GLN* 2.9 45.3 + - + +
162J LYS* 3.5 59.8 + - + -
241J ALA* 3.9 15.5 - - + +
242J VAL 3.3 12.6 - - - -
243J LYS* 4.0 16.4 - - + +
285J TYR* 3.9 16.6 - + - -
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Residues in contact with LEU 94 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58J PRO 3.4 26.7 - - - +
59J THR* 3.8 17.3 - - + -
61J GLY* 3.9 4.3 - - - -
62J VAL* 3.8 21.8 - - + +
93J TYR* 1.3 77.9 - - - +
95J GLU* 1.3 75.3 + - - +
96J LEU* 4.2 9.9 - - + -
138J CYS* 4.0 12.1 - - + -
139J HIS 3.3 9.0 - - - +
140J ASN* 3.4 27.4 - - - +
220J PHE* 5.3 0.2 - - + -
239J PHE* 5.8 2.7 - - + -
241J ALA* 3.0 5.4 - - - +
242J VAL* 2.9 43.9 + - + +
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Residues in contact with GLU 95 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93J TYR* 2.9 29.5 + - + +
94J LEU* 1.3 74.6 - - - +
96J LEU* 1.3 68.0 + - - +
97J TYR* 3.5 44.5 + - + -
138J CYS* 3.2 6.8 - - - +
139J HIS* 2.9 35.1 + - + +
162J LYS* 4.6 5.5 + - - -
240J LYS* 3.2 13.5 - - + +
241J ALA* 3.8 8.3 - - + -
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Residues in contact with LEU 96 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58J PRO* 3.4 46.2 - - + +
94J LEU* 4.2 12.6 - - + -
95J GLU* 1.3 77.2 - - - +
97J TYR* 1.3 63.9 + - - +
98J LYS* 3.0 12.9 + - - +
99J PRO* 5.2 2.2 - - + -
100J LEU* 3.9 26.5 - - + +
137J ILE 3.7 2.2 - - - -
138J CYS* 3.8 21.8 - - + -
236J VAL* 5.4 1.6 - - + +
239J PHE* 3.5 29.0 - - + +
240J LYS* 2.6 23.2 + - - +
241J ALA* 5.8 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