Contacts of the strand formed by residues 113 - 118 (chain J) in PDB entry 3STJ
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 ILE 113 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78J LEU* 3.8 22.9 - - + -
79J THR 3.7 7.6 - - - +
80J ASN* 5.3 0.4 - - - +
81J ASN* 4.1 1.3 - - - +
107J SER* 3.3 2.6 - - - -
108J ASP* 2.7 35.8 + - + +
111J SER* 3.9 9.2 + - - +
112J ASP* 1.3 80.9 - - - +
114J ALA* 1.3 61.2 + - - +
201J ILE* 5.3 4.0 - - + -
219J ILE* 3.5 39.9 - - + -
224J ALA* 3.7 22.7 - - + +
227J LEU* 3.9 31.6 - - + -
231J LEU* 4.2 13.9 - - + -
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Residues in contact with ALA 114 (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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78J LEU* 3.6 8.3 - - - +
79J THR* 3.0 48.7 + - + +
80J ASN 3.8 11.9 - - - +
81J ASN* 3.9 9.6 - - - +
84J ILE* 3.9 15.0 - - + -
104J LEU* 4.2 3.1 - - + -
106J GLY 3.5 6.1 - - - +
107J SER* 4.0 7.9 - - - +
113J ILE* 1.3 77.2 - - - +
115J LEU* 1.3 60.8 + - - +
231J LEU* 4.6 0.2 - - - -
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Residues in contact with LEU 115 (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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70J ILE* 4.4 7.2 - - + -
76J TYR* 4.3 23.3 - - + -
77J VAL 3.5 18.8 - - - +
78J LEU* 4.4 7.0 - - + +
104J LEU* 3.5 4.0 - - - +
105J ILE* 2.8 52.8 + - + -
106J GLY 2.8 14.1 + - - +
114J ALA* 1.3 74.9 - - - +
116J LEU* 1.3 60.9 + - - +
228J ALA* 4.3 22.4 - - + +
231J LEU* 4.0 16.8 - - + +
232J ILE* 3.6 33.2 - - + +
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Residues in contact with LEU 116 (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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29J VAL* 3.9 8.3 - - + -
75J GLY 3.4 0.5 - - - +
76J TYR* 3.5 4.9 - - - -
77J VAL* 2.8 45.5 + - + +
79J THR* 3.8 25.4 - - + -
84J ILE* 3.7 23.8 - - + -
90J ILE* 3.9 19.5 - - + -
92J ILE* 3.8 26.2 - - + -
102J ALA* 4.4 7.9 - - + -
103J LYS 3.4 5.8 - - - +
104J LEU* 3.8 27.8 - - + -
105J ILE* 4.1 3.6 - - - -
115J LEU* 1.3 76.9 - - - +
117J GLN* 1.3 60.6 + - - +
118J ILE 4.2 0.2 - - - -
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Residues in contact with GLN 117 (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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74J LYS* 3.0 37.9 + - - +
75J GLY 3.3 2.9 - - - +
76J TYR* 3.6 24.4 + - + -
102J ALA* 3.3 3.0 - - - -
103J LYS 2.9 31.9 + - - +
105J ILE* 3.5 29.1 - - + +
116J LEU* 1.3 74.7 - - - +
118J ILE* 1.3 63.8 + - - +
119J GLN* 3.1 18.1 + - - +
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Residues in contact with ILE 118 (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 ILE* 4.4 6.7 - - + -
74J LYS 4.1 0.3 - - - +
75J GLY* 2.8 19.7 + - - +
77J VAL* 3.6 27.6 - - + -
92J ILE* 4.0 29.4 - - + -
94J LEU* 5.2 0.4 - - + -
100J PHE* 3.5 35.9 - - + -
101J ASP 3.5 5.6 - - - +
102J ALA* 4.4 2.0 - - + +
116J LEU* 6.4 0.2 - - + -
117J GLN* 1.3 81.1 - - - +
119J GLN* 1.3 62.4 + - - +
120J ASN 3.6 0.2 + - - -
121J PRO* 3.3 32.0 - - + +
124J LEU* 3.7 26.7 - - + -
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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