Contacts of the strand formed by residues 110 - 115 (chain A) in PDB entry 3TJK
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 TYR 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A TYR* 5.5 0.5 - - - -
109A LYS* 1.3 79.8 - - - +
111A LEU* 1.3 60.3 + - - +
142A ASN* 3.3 6.3 + - - -
143A THR* 3.4 25.1 - - + +
144A GLU* 3.1 22.5 + - - +
204A ILE* 3.8 22.2 - - + -
205A ILE 3.3 13.0 - - - -
206A ASP* 3.3 24.4 - - + +
207A ASP* 3.7 12.8 - - + -
212A ARG* 3.0 21.2 + - + -
232A VAL* 4.2 7.9 - - + -
235A PHE* 3.4 24.1 - - + +
236A GLN* 3.7 28.0 - - + +
239A ASP* 2.4 31.3 + - - -
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Residues in contact with LEU 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A TRP* 4.2 7.2 - - + -
103A LEU* 3.7 30.3 - - + -
106A TYR* 4.1 35.9 - - + -
109A LYS 4.7 0.9 - - - +
110A TYR* 1.3 76.9 - - - +
112A VAL* 1.3 78.6 + - - +
113A PHE* 4.1 14.6 - - + +
144A GLU 3.5 14.8 - - - +
146A VAL* 3.7 27.1 - - + -
203A PHE 3.5 1.4 - - - +
204A ILE* 3.5 5.4 - - - +
205A ILE* 2.7 45.5 + - + +
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Residues in contact with VAL 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A LEU* 1.3 75.7 - - - +
113A PHE* 1.3 59.8 + - - +
114A PHE* 4.5 4.5 - - + -
131A PHE* 4.2 10.1 - - + -
138A PHE* 4.2 6.5 - - + -
143A THR* 4.2 9.4 - - + -
144A GLU 2.9 11.6 + - - +
145A VAL* 3.4 13.1 - - + +
146A VAL 3.0 26.7 + - - +
202A LEU* 3.7 33.2 - - + -
203A PHE 3.5 3.4 - - - +
204A ILE* 4.5 5.2 - - + -
228A THR* 3.8 23.1 - - + -
232A VAL* 3.9 20.9 - - + -
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Residues in contact with PHE 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A TRP* 3.4 53.6 - + - -
111A LEU* 3.7 7.4 - - + -
112A VAL* 1.3 72.7 - - - +
114A PHE* 1.3 62.0 + - - +
115A PHE* 3.4 36.8 - + - -
146A VAL* 3.5 17.9 - - + -
148A CYS* 4.2 8.7 - - + -
177A LEU* 3.8 16.8 - - + -
184A ILE* 4.0 9.2 - - + -
188A TYR* 3.8 24.0 - + - -
203A PHE* 2.8 44.1 + + + +
205A ILE* 4.1 15.5 - - + -
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Residues in contact with PHE 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A VAL* 4.5 5.6 - - + -
113A PHE* 1.3 77.6 - - - +
115A PHE* 1.3 65.2 + - - +
116A TYR* 4.3 6.1 - + + -
127A GLU* 4.5 8.5 - - + -
128A ILE* 4.0 26.5 - - + -
131A PHE* 3.7 33.7 - + + -
145A VAL* 3.9 21.3 - - + -
146A VAL 2.9 16.0 + - - -
147A ALA* 3.2 32.8 - - + -
148A CYS* 2.8 25.8 + - - +
174A ILE* 5.2 2.2 - - + -
201A GLY 3.4 9.9 - - - +
202A LEU* 3.8 16.4 - - + -
223A ARG* 3.5 32.1 - - - +
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Residues in contact with PHE 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A PHE* 3.4 31.9 - + - -
114A PHE* 1.3 76.9 - - - +
116A TYR* 1.3 57.0 + - - +
148A CYS* 3.1 37.5 - - + +
149A SER* 5.3 0.2 - - - -
184A ILE* 3.9 12.8 - - + -
185A SER* 3.9 11.9 - - - -
188A TYR* 3.7 22.4 - + + -
190A VAL* 3.8 17.9 - - + -
198A THR* 3.6 23.3 - - + +
199A LEU 4.0 6.1 - - - +
200A ARG* 3.8 0.3 - - - -
201A GLY 2.8 22.2 + - - +
203A PHE* 3.6 23.3 - + - -
223A ARG* 2.7 33.2 + - - -
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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