Contacts of the strand formed by residues 331 - 338 (chain A) in PDB entry 2P80
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 MET 331 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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326A TRP* 2.7 41.4 + - + -
327A ASN 3.3 2.0 + - - -
328A ASP 2.9 7.0 + - - +
330A LEU* 1.3 83.3 - - - +
332A THR* 1.3 66.6 + - - +
102C ALA* 3.5 32.3 - - + -
103C THR 4.0 11.2 - - - +
104C GLY 2.8 32.1 - - - +
105C ALA* 3.6 15.7 - - - -
107C GLY 4.1 0.2 - - - -
108C GLY* 3.7 13.0 - - - +
111C LEU* 4.0 2.0 - - + -
122C LEU* 3.5 27.6 - - + -
123C ARG 3.4 8.7 - - - +
124C PHE* 4.2 4.5 - - + -
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Residues in contact with THR 332 (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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326A TRP* 4.8 1.3 - - - +
328A ASP* 2.3 39.7 + - - +
331A MET* 1.3 78.0 - - - +
333A SER* 1.3 60.7 + - - +
334A VAL* 3.1 17.0 + - + +
111C LEU* 5.8 0.7 - - - -
122C LEU* 3.9 4.2 - - - -
123C ARG* 3.0 58.1 + - - +
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Residues in contact with SER 333 (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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332A THR* 1.3 72.4 + - - +
334A VAL* 1.3 66.4 + - - +
335A LEU* 3.6 3.5 + - - -
336A ALA* 3.5 30.8 + - - +
337A PRO* 4.7 0.2 - - - +
111C LEU* 4.0 37.9 + - - +
121C ILE 3.8 5.9 + - - -
122C LEU* 4.4 5.1 - - - +
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Residues in contact with VAL 334 (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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332A THR* 3.1 12.4 + - + +
333A SER* 1.3 73.9 - - - +
335A LEU* 1.3 64.7 + - + +
336A ALA 4.2 0.3 + - - -
82C GLU* 3.5 28.5 - - - +
121C ILE* 2.9 28.3 + - + +
123C ARG* 4.0 22.0 - - + +
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Residues in contact with LEU 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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333A SER* 3.6 3.3 + - - -
334A VAL* 1.3 83.5 - - + +
336A ALA* 1.3 60.0 + - - +
338A SER* 4.0 13.7 - - - +
339A GLY 5.9 0.7 - - - +
119C LYS* 3.9 39.0 - - + +
120C THR* 2.1 34.1 + - - -
121C ILE* 3.0 33.9 + - + +
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Residues in contact with ALA 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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333A SER* 3.5 14.4 + - - +
334A VAL 4.1 1.4 + - - -
335A LEU* 1.3 81.0 - - - +
337A PRO* 1.3 81.7 - - + +
338A SER* 3.0 15.1 + - - -
119C LYS 4.1 0.3 - - - +
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Residues in contact with PRO 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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333A SER* 4.7 0.2 - - - +
335A LEU 3.6 0.4 - - - -
336A ALA* 1.3 89.3 - - + +
338A SER* 1.3 61.8 + - - +
111C LEU* 4.1 13.2 - - - +
112C THR 4.3 1.6 - - - -
113C GLU* 3.1 38.6 - - + +
114C ILE* 3.4 23.6 - - + -
118C GLU* 4.2 9.5 - - - +
120C THR* 3.8 11.0 - - - +
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Residues in contact with SER 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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335A LEU* 4.0 16.5 - - - +
336A ALA 3.0 12.9 + - - -
337A PRO* 1.3 75.9 - - - +
339A GLY* 1.3 73.5 + - - +
118C GLU* 3.2 16.8 - - - +
119C LYS 3.0 25.9 + - - +
106D LYS* 5.9 0.7 - - - +
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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