Contacts of the strand formed by residues 334 - 339 (chain A) in PDB entry 3TMP
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 HIS 334 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A GLN* 5.1 2.0 + - - -
218A MET 3.2 20.1 + - - -
219A LYS 3.7 4.7 - - - -
220A GLU* 3.7 30.1 + - + +
224A CYS* 3.6 11.1 - - + +
328A SER 3.6 0.3 - - - +
329A TYR* 3.4 6.2 - - - -
330A HIS* 2.7 40.5 + - + +
331A ARG* 3.9 20.0 - - - +
333A ILE* 1.3 80.7 - - - +
335A TYR* 1.3 77.5 + - - +
336A ASN* 3.0 37.3 + - - -
76B GLZ 2.9 23.3 + - - +
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Residues in contact with TYR 335 (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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218A MET* 3.6 9.5 - - - +
224A CYS* 3.5 11.3 - - - +
225A LEU* 3.8 40.4 - - + -
228A ALA* 4.6 3.1 - - + -
280A GLY 4.8 1.8 - - - -
285A MET* 3.1 26.2 - - + +
298A VAL* 4.4 3.8 - - + +
327A VAL* 3.9 25.6 - - + -
328A SER 3.2 14.1 - - - -
329A TYR* 3.5 31.0 - + + -
334A HIS* 1.3 96.3 + - - +
336A ASN* 1.3 62.8 + - - +
73B LEU* 2.7 36.1 + - - +
75B GLY* 3.6 26.2 - - - -
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Residues in contact with ASN 336 (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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215A ILE* 4.1 6.0 - - + +
216A LYS 3.4 9.2 - - - +
217A GLN* 3.5 28.3 + - - +
218A MET* 2.7 30.8 + - - +
228A ALA* 3.5 11.1 - - - +
327A VAL* 3.4 6.6 - - - +
328A SER* 2.9 40.4 + - - +
330A HIS* 3.2 26.4 + - - +
331A ARG* 5.8 0.6 - - - +
334A HIS* 3.0 21.1 + - - -
335A TYR* 1.3 72.1 - - - +
337A SER* 1.3 60.2 + - - +
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Residues in contact with SER 337 (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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215A ILE* 3.7 3.5 - - - +
216A LYS* 2.7 39.8 + - - +
218A MET* 3.5 23.1 - - - +
228A ALA* 4.2 6.5 - - - -
231A ASP* 2.8 32.9 + - - +
232A GLN* 3.0 20.1 + - - +
326A ARG 4.1 3.1 - - - -
336A ASN* 1.3 75.6 - - - +
338A VAL* 1.3 59.5 + - - +
339A VAL* 4.1 2.4 - - - +
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Residues in contact with VAL 338 (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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207A LEU* 5.1 3.1 - - + -
213A PHE* 3.6 40.6 - - + -
214A ILE 3.6 3.6 - - - +
215A ILE* 3.8 11.9 - - + -
232A GLN* 2.9 18.2 + - - +
299A TYR* 4.1 13.2 - - + -
326A ARG* 3.0 37.7 + - + +
327A VAL 3.7 11.7 - - - +
328A SER* 3.6 31.2 - - - +
336A ASN 4.0 0.2 + - - -
337A SER* 1.3 69.6 + - - +
339A VAL* 1.3 61.3 + - - +
340A ASN 4.0 1.0 + - - -
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Residues in contact with VAL 339 (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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213A PHE* 3.2 8.7 - - - -
214A ILE* 2.8 48.5 + - + +
216A LYS* 4.0 30.3 - - + +
231A ASP* 4.0 15.5 - - - +
232A GLN* 4.4 4.0 - - - +
337A SER* 4.1 2.7 - - - +
338A VAL* 1.3 73.7 - - - +
340A ASN* 1.3 73.5 + - - +
341A PRO* 3.5 14.2 - - + +
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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