Contacts of the strand formed by residues 97 - 101 (chain B) in PDB entry 4TLG
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 PRO 97 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B LEU* 5.2 1.6 - - + -
90B GLY 3.7 7.9 - - - +
91B TYR* 3.7 7.0 - - + -
95B GLY 3.5 5.6 - - - +
96B CYS* 1.3 83.1 - - - +
98B VAL* 1.3 59.9 + - - +
131B LEU* 3.9 21.8 - - + +
134B GLU* 3.8 29.2 - - + +
135B CYS* 3.7 26.2 - - - +
138B GLN* 5.1 0.4 - - + -
146B ILE* 4.4 2.7 - - + -
148B MET 3.7 11.0 - - - +
149B ALA* 3.3 13.8 - - + +
150B LEU 2.9 25.1 + - - -
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Residues in contact with VAL 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B LEU* 3.5 7.3 - - - +
89B CYS 3.0 41.4 + - - +
90B GLY 2.9 17.2 + - - +
91B TYR 4.0 0.9 - - - -
92B ASP 3.9 18.4 - - - +
96B CYS 4.0 0.7 - - - +
97B PRO* 1.3 76.8 - - - +
99B TYR* 1.3 67.2 + - - +
100B PHE* 3.7 20.9 - - + -
131B LEU* 4.5 1.7 - - - +
150B LEU* 3.3 16.4 - - + +
152B VAL* 4.1 8.7 - - + -
232B ILE* 3.8 32.5 - - + -
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Residues in contact with TYR 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B SER 3.6 7.6 + - - -
86B GLY* 3.5 16.3 - - - -
87B GLY* 3.3 31.6 - - - -
88B LEU* 3.6 10.1 - - + -
98B VAL* 1.3 75.1 - - - +
100B PHE* 1.3 78.5 + - - +
101B ASN* 4.0 18.3 - - + -
123B LYS* 3.7 8.3 + - - -
127B VAL* 3.5 46.7 - - + +
131B LEU* 3.9 21.1 - - + +
150B LEU 2.9 7.1 + - - -
151B MET* 3.3 24.0 - - + -
152B VAL* 2.8 27.7 + - - +
504B EDO 4.0 5.1 + - - -
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Residues in contact with PHE 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B GLY* 3.0 7.7 - - - -
87B GLY 2.9 41.7 + - - +
89B CYS* 3.6 28.7 - - + -
98B VAL* 3.7 13.7 - - + -
99B TYR* 1.3 79.4 - - - +
101B ASN* 1.3 59.8 + - - +
102B ILE* 4.0 13.7 - - + -
152B VAL* 3.5 30.3 - - + -
154B ASP* 5.9 0.7 - - + -
228B LEU* 5.0 1.3 - - + -
236B GLN 5.5 0.2 - - - -
237B LEU* 3.8 27.4 - - + -
238B PRO* 4.1 12.8 - - + -
241B PHE* 3.6 37.2 - + + -
258B ILE* 4.0 19.3 - - + -
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Residues in contact with ASN 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B SER* 4.5 6.4 + - - +
86B GLY* 4.5 1.6 - - - -
99B TYR* 3.9 19.7 + - + -
100B PHE* 1.3 72.3 - - - +
102B ILE* 1.3 62.0 + - - +
103B ILE* 2.9 30.9 + - - +
106B LEU* 5.9 0.3 - - - +
151B MET* 5.5 3.3 - - - -
152B VAL 2.7 14.2 + - - +
153B PHE* 3.5 27.2 - - + -
154B ASP* 2.8 28.6 + - - +
171B TYR* 3.1 26.2 + - - -
174B PHE* 5.9 1.8 - - - -
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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