Contacts of the strand formed by residues 113 - 118 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78H LEU* 3.8 23.3 - - + -
79H THR 3.7 7.4 - - - +
80H ASN* 5.1 0.4 - - - +
81H ASN* 4.1 2.0 - - - +
107H SER* 3.3 1.7 - - - -
108H ASP* 2.7 36.7 + - + +
111H SER* 3.6 9.3 + - - +
112H ASP* 1.3 80.7 - - - +
114H ALA* 1.3 61.6 + - - +
201H ILE* 5.2 4.3 - - + -
219H ILE* 3.5 39.9 - - + -
224H ALA* 3.7 22.4 - - + +
227H LEU* 3.8 31.2 - - + -
228H ALA 4.8 1.1 - - - +
231H LEU* 4.2 12.7 - - + +
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Residues in contact with ALA 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78H LEU* 3.7 6.1 - - - +
79H THR* 3.0 38.7 + - + +
80H ASN 4.2 4.0 - - - +
81H ASN* 3.9 11.2 - - - +
84H ILE* 3.9 23.3 - - + -
104H LEU* 4.0 4.3 - - + -
106H GLY 3.4 7.4 - - - +
107H SER* 3.8 16.8 - - - +
113H ILE* 1.3 77.6 - - - +
115H LEU* 1.3 59.0 + - - +
231H LEU* 4.6 0.2 - - - -
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Residues in contact with LEU 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70H ILE* 4.3 7.0 - - + -
76H TYR* 4.2 22.0 - - + -
77H VAL 3.5 19.1 - - - +
78H LEU* 4.4 5.4 - - + +
104H LEU* 3.5 4.5 - - - +
105H ILE* 2.8 53.5 + - + -
106H GLY 2.8 12.3 + - - +
114H ALA* 1.3 73.9 - - - +
116H LEU* 1.3 61.5 + - - +
228H ALA* 4.1 26.9 - - + +
231H LEU* 3.9 18.3 - - + +
232H ILE* 3.5 31.9 - - + +
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Residues in contact with LEU 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H VAL* 4.4 3.4 - - + -
76H TYR* 3.3 8.8 - - - -
77H VAL* 2.8 47.4 + - + +
79H THR* 3.9 15.5 - - + -
84H ILE* 3.7 41.5 - - + -
90H ILE* 3.9 12.3 - - + -
92H ILE* 3.9 25.8 - - + -
102H ALA* 4.3 8.3 - - + -
103H LYS 3.4 5.8 - - - +
104H LEU* 3.8 27.4 - - + -
105H ILE* 4.1 2.9 - - - -
115H LEU* 1.3 75.3 - - - +
117H GLN* 1.3 60.1 + - - +
118H ILE 4.2 0.2 - - - -
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Residues in contact with GLN 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74H LYS* 2.9 35.7 + - - +
75H GLY 3.3 2.7 - - - -
76H TYR* 3.5 26.3 + - + -
102H ALA* 3.3 3.0 - - - -
103H LYS* 2.9 33.8 + - + +
105H ILE* 3.5 29.7 - - + +
116H LEU* 1.3 73.2 - - - +
118H ILE* 1.3 64.7 + - - +
119H GLN* 3.1 17.5 + - - +
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Residues in contact with ILE 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69H ILE* 4.5 5.8 - - + -
74H LYS 4.2 0.3 - - - +
75H GLY* 2.7 20.2 + - - +
77H VAL* 3.6 27.8 - - + -
92H ILE* 4.0 29.6 - - + -
94H LEU* 5.3 0.2 - - + -
100H PHE* 3.5 36.8 - - + -
101H ASP 3.5 5.8 - - - +
102H ALA* 4.3 2.9 - - + +
117H GLN* 1.3 80.1 - - - +
119H GLN* 1.3 63.0 + - - +
120H ASN 3.6 0.2 + - - -
121H PRO* 3.3 31.7 - - + +
124H 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