Contacts of the strand formed by residues 113 - 118 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78C LEU* 3.8 20.6 - - + -
79C THR 3.6 7.6 - - - +
80C ASN* 5.1 0.7 - - - +
81C ASN* 4.1 1.7 - - - +
107C SER* 3.3 2.3 - - - -
108C ASP* 2.7 37.1 + - + +
111C SER* 3.6 8.7 + - - +
112C ASP* 1.3 81.0 - - - +
114C ALA* 1.3 59.8 + - - +
201C ILE* 5.3 3.4 - - + -
219C ILE* 3.6 39.9 - - + -
224C ALA* 3.7 23.3 - - + +
227C LEU* 3.8 30.7 - - + -
228C ALA 4.8 1.3 - - - +
231C LEU* 4.2 14.8 - - + +
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Residues in contact with ALA 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C LEU* 3.5 5.5 - - - +
79C THR* 3.0 43.2 + - + +
81C ASN* 3.8 23.1 - - - +
84C ILE* 3.9 20.2 - - + -
104C LEU* 4.2 3.6 - - + -
106C GLY 3.5 6.7 - - - +
107C SER* 4.0 7.0 - - - +
113C ILE* 1.3 76.8 - - - +
115C LEU* 1.3 60.0 + - - +
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Residues in contact with LEU 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C ILE* 4.3 6.1 - - + -
76C TYR* 4.2 21.8 - - + -
77C VAL 3.6 19.7 - - - +
78C LEU* 4.3 7.0 - - + +
104C LEU* 3.5 3.8 - - - +
105C ILE* 2.8 53.7 + - + -
106C GLY 2.8 14.4 + - - +
114C ALA* 1.3 73.9 - - - +
116C LEU* 1.3 60.2 + - - +
228C ALA* 4.2 26.0 - - + +
231C LEU* 3.9 18.8 - - + +
232C ILE* 3.4 32.1 - - + +
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Residues in contact with LEU 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C VAL* 4.2 6.7 - - + -
76C TYR* 3.4 7.8 - - - -
77C VAL* 2.8 44.0 + - + +
79C THR* 3.9 16.8 - - + -
84C ILE* 3.7 40.2 - - + -
90C ILE* 3.9 13.5 - - + -
92C ILE* 3.9 25.8 - - + -
102C ALA* 4.4 8.3 - - + -
103C LYS 3.4 5.8 - - - +
104C LEU* 3.8 27.1 - - + -
105C ILE* 4.1 3.4 - - - -
115C LEU* 1.3 75.6 - - - +
117C GLN* 1.3 60.5 + - - +
118C ILE 4.2 0.2 - - - -
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Residues in contact with GLN 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C LYS* 2.9 36.7 + - - +
75C GLY 3.3 2.5 - - - +
76C TYR* 3.5 24.7 + - + -
102C ALA* 3.2 4.1 - - - -
103C LYS 2.9 31.5 + - - +
105C ILE* 3.4 30.4 - - + +
116C LEU* 1.3 73.1 - - - +
118C ILE* 1.3 65.1 + - - +
119C GLN* 3.1 17.3 + - - +
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Residues in contact with ILE 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C ILE* 4.5 6.3 - - + -
74C LYS 4.2 0.2 - - - +
75C GLY* 2.7 19.8 + - - +
77C VAL* 3.6 27.1 - - + -
92C ILE* 4.0 29.8 - - + -
94C LEU* 5.2 0.4 - - + -
100C PHE* 3.5 36.1 - - + -
101C ASP 3.5 5.4 - - - +
102C ALA* 4.4 1.8 - - + +
116C LEU 4.2 0.2 - - - -
117C GLN* 1.3 82.4 - - - +
119C GLN* 1.3 63.4 + - - +
120C ASN 3.6 0.2 + - - -
121C PRO* 3.3 30.9 - - + +
124C 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