Contacts of the strand formed by residues 113 - 118 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78L LEU* 3.8 22.9 - - + -
79L THR 3.8 7.6 - - - +
81L ASN* 4.1 1.3 - - - +
107L SER* 3.3 1.6 - - - -
108L ASP* 2.7 36.1 + - + +
111L SER* 3.5 9.1 + - - +
112L ASP* 1.3 81.2 - - - +
114L ALA* 1.3 59.6 + - - +
201L ILE* 5.3 4.5 - - + -
219L ILE* 3.5 41.3 - - + -
224L ALA* 3.7 21.3 - - + +
227L LEU* 3.8 32.3 - - + -
228L ALA 4.7 0.7 - - - +
231L LEU* 4.2 13.5 - - + -
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Residues in contact with ALA 114 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77L VAL 3.9 0.3 - - - +
78L LEU* 3.8 4.9 - - - +
79L THR* 3.0 38.2 + - + +
80L ASN 3.8 8.5 - - - +
81L ASN* 3.8 20.6 - - - +
84L ILE* 3.8 14.4 - - + -
104L LEU* 4.1 3.1 - - + -
106L GLY 3.5 5.8 - - - +
107L SER* 3.8 13.0 - - - -
113L ILE* 1.3 78.5 - - - +
115L LEU* 1.3 60.1 + - - +
116L LEU* 5.2 0.2 - - + -
231L LEU* 4.6 0.2 - - - -
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Residues in contact with LEU 115 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70L ILE* 4.3 7.6 - - + -
76L TYR* 4.2 21.5 - - + -
77L VAL 3.5 18.2 - - - +
78L LEU* 4.4 6.1 - - + +
104L LEU* 3.5 4.2 - - - +
105L ILE* 2.8 53.4 + - + -
106L GLY 2.8 14.4 + - - +
114L ALA* 1.3 72.8 - - - +
116L LEU* 1.3 60.5 + - - +
228L ALA* 4.1 25.8 - - + +
231L LEU* 4.0 17.2 - - + +
232L ILE* 3.4 31.9 - - + +
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Residues in contact with LEU 116 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29L VAL* 4.3 3.1 - - + -
75L GLY 4.2 0.2 - - - -
76L TYR* 3.3 8.8 - - - -
77L VAL* 2.8 46.9 + - + +
79L THR* 3.8 24.0 - - + -
84L ILE* 3.7 31.9 - - + -
90L ILE* 3.9 13.7 - - + -
92L ILE* 3.9 25.6 - - + -
102L ALA* 4.4 8.5 - - + -
103L LYS 3.4 5.2 - - - +
104L LEU* 3.8 27.4 - - + -
105L ILE* 4.1 3.4 - - - -
114L ALA* 5.2 0.2 - - + -
115L LEU* 1.3 75.7 - - - +
117L GLN* 1.3 60.0 + - - +
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Residues in contact with GLN 117 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74L LYS* 2.9 36.5 + - - +
75L GLY 3.3 2.2 - - - -
76L TYR* 3.6 25.5 + - + -
102L ALA* 3.3 3.6 - - - -
103L LYS 2.8 32.7 + - - +
105L ILE* 3.5 30.5 - - + +
116L LEU* 1.3 73.2 - - - +
118L ILE* 1.3 64.4 + - - +
119L GLN* 3.1 17.0 + - - +
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Residues in contact with ILE 118 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69L ILE* 4.5 5.6 - - + -
74L LYS 4.2 0.3 - - - +
75L GLY* 2.8 19.8 + - - +
77L VAL* 3.7 28.0 - - + -
92L ILE* 4.0 29.6 - - + -
94L LEU* 5.2 0.4 - - + -
100L PHE* 3.5 35.9 - - + -
101L ASP 3.5 5.2 - - - +
102L ALA* 4.4 2.2 - - + +
117L GLN* 1.3 82.7 - - - +
119L GLN* 1.3 62.1 + - - +
121L PRO* 3.3 31.7 - - + +
124L LEU* 3.7 27.4 - - + -
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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