Contacts of the strand formed by residues 113 - 118 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78I LEU* 3.8 24.2 - - + -
79I THR 3.6 7.0 - - - +
80I ASN* 5.1 0.2 - - - +
81I ASN* 4.1 1.2 - - - +
107I SER* 3.3 2.4 - - - -
108I ASP* 2.7 36.5 + - + +
111I SER* 3.9 8.7 + - - +
112I ASP* 1.3 81.4 - - - +
114I ALA* 1.3 62.0 + - - +
201I ILE* 5.3 4.0 - - + -
219I ILE* 3.5 40.8 - - + -
224I ALA* 3.7 22.0 - - + +
227I LEU* 3.8 30.7 - - + -
228I ALA 4.8 0.7 - - - +
231I LEU* 4.1 14.1 - - + +
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Residues in contact with ALA 114 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78I LEU* 3.5 9.0 - - - +
79I THR* 2.9 37.4 + - + +
80I ASN 3.9 7.0 - - - +
81I ASN* 3.8 22.9 - - - +
84I ILE* 3.9 17.0 - - + -
104I LEU* 4.2 4.3 - - + -
106I GLY 3.6 5.8 - - - +
107I SER* 4.0 7.6 - - - +
113I ILE* 1.3 77.4 - - - +
115I LEU* 1.3 61.2 + - - +
231I LEU* 4.5 0.2 - - - -
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Residues in contact with LEU 115 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70I ILE* 4.3 7.9 - - + -
76I TYR* 4.2 21.8 - - + -
77I VAL 3.5 18.4 - - - +
78I LEU* 4.4 6.3 - - + +
104I LEU* 3.6 3.6 - - - +
105I ILE* 2.8 53.6 + - + -
106I GLY 2.8 14.8 + - - +
114I ALA* 1.3 73.7 - - - +
116I LEU* 1.3 60.7 + - - +
228I ALA* 4.2 24.5 - - + +
231I LEU* 4.0 17.9 - - + +
232I ILE* 3.5 31.2 - - + +
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Residues in contact with LEU 116 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29I VAL* 4.3 6.7 - - + -
75I GLY 4.2 0.2 - - - -
76I TYR* 3.3 8.7 - - - -
77I VAL* 2.8 43.2 + - + +
79I THR* 3.8 24.9 - - + -
84I ILE* 3.7 26.9 - - + -
90I ILE* 3.9 19.5 - - + -
92I ILE* 3.8 25.8 - - + -
102I ALA* 4.4 7.6 - - + -
103I LYS 3.4 5.8 - - - +
104I LEU* 3.8 27.4 - - + -
105I ILE* 4.1 3.4 - - - -
115I LEU* 1.3 73.5 - - - +
117I GLN* 1.3 61.7 + - - +
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Residues in contact with GLN 117 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74I LYS* 3.0 36.2 + - - +
75I GLY 3.3 2.2 - - - +
76I TYR* 3.5 25.1 + - + -
102I ALA* 3.3 3.7 - - - -
103I LYS 2.9 31.2 + - - +
105I ILE* 3.5 29.6 - - + +
116I LEU* 1.3 74.5 - - - +
118I ILE* 1.3 67.8 + - - +
119I GLN* 3.1 17.2 + - - +
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Residues in contact with ILE 118 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69I ILE* 4.5 5.8 - - + -
75I GLY* 2.7 20.2 + - - +
77I VAL* 3.7 27.8 - - + -
92I ILE* 4.0 30.3 - - + -
94I LEU* 5.2 0.2 - - + -
100I PHE* 3.5 36.3 - - + -
101I ASP 3.5 5.4 - - - +
102I ALA* 4.4 2.0 - - + +
117I GLN* 1.3 82.6 - - - +
119I GLN* 1.3 64.6 + - - +
121I PRO* 3.3 30.8 - - + +
124I 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