Contacts of the strand formed by residues 672 - 681 (chain B) in PDB entry 2PMW
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 VAL 672 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614B GLY* 3.4 0.4 - - - -
615B ILE 2.8 37.2 + - - -
616B PRO 4.6 0.2 + - - -
618B PRO* 3.7 24.0 - - + -
622B VAL* 3.7 27.5 - - + +
637B ALA* 5.3 1.8 - - + -
638B LEU 6.0 0.4 - - - -
642B SER* 3.7 24.2 - - - +
644B VAL* 4.5 6.7 - - + -
656B VAL* 3.9 28.7 - - + +
658B SER* 4.2 11.7 - - - -
671B ALA* 1.3 75.5 - - - +
673B THR* 1.3 62.6 + - - +
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Residues in contact with THR 673 (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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612B GLU* 4.1 12.6 - - + +
613B HIS 3.3 20.4 - - - +
614B GLY* 3.5 11.9 - - - +
637B ALA* 3.5 6.4 - - - +
638B LEU* 3.0 54.0 + - + +
656B VAL* 4.8 0.2 - - - -
671B ALA* 4.2 5.5 + - - +
672B VAL* 1.3 78.3 - - - +
674B ALA* 1.3 72.3 + - - +
675B VAL* 4.2 6.7 - - + -
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Residues in contact with ALA 674 (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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612B GLU* 3.3 4.2 - - - -
613B HIS 2.8 37.4 + - - +
622B VAL* 3.8 21.0 - - + +
623B THR* 4.1 2.5 - - - -
624B VAL* 3.7 26.2 - - + +
654B CYS* 4.3 4.3 - - - +
656B VAL* 3.8 23.1 - - + +
673B THR* 1.3 74.2 - - - +
675B VAL* 1.3 60.2 + - - +
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Residues in contact with VAL 675 (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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610B VAL* 3.6 28.0 - - + -
611B LYS 3.6 2.5 - - - -
612B GLU* 4.0 16.2 - - + +
634B GLY 3.7 1.2 - - - +
635B CYS* 3.5 4.3 - - - -
636B SER* 2.9 48.4 + - - +
637B ALA 4.6 0.7 - - - -
638B LEU* 4.0 32.1 - - + +
654B CYS* 3.6 3.2 - - - -
673B THR* 4.0 9.2 - - + +
674B ALA* 1.3 78.7 - - - +
676B ALA* 1.3 62.1 + - - +
677B ILE* 4.1 6.2 + - + +
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Residues in contact with ALA 676 (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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609B LYS 3.8 0.5 - - - +
610B VAL* 3.4 6.0 - - - +
611B LYS* 2.9 38.1 + - + +
624B VAL* 3.8 24.5 - - + +
626B CYS* 4.4 2.5 - - - +
632B LEU* 3.4 21.5 - - + -
634B GLY 3.3 3.8 - - - -
654B CYS* 3.9 6.3 - - + -
675B VAL* 1.3 73.7 - - - +
677B ILE* 1.3 61.5 + - - +
678B CYS* 4.0 11.3 + - - -
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Residues in contact with ILE 677 (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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559B LEU* 3.6 33.9 - - + +
560B THR* 3.6 23.6 - - - +
561B GLY* 3.6 15.9 - - - +
562B CYS* 4.3 7.0 - - + +
608B CYS* 4.5 3.6 - - + -
609B LYS 3.6 8.3 - - - +
610B VAL* 4.3 17.7 - - + -
632B LEU* 3.5 4.3 - - - +
633B THR* 2.8 43.9 + - - +
634B GLY* 2.8 19.3 + - - +
636B SER* 6.1 0.9 - - - +
675B VAL* 5.3 5.4 - - + +
676B ALA* 1.3 73.7 - - - +
678B CYS* 1.3 62.6 - - - +
679B CYS* 4.4 7.4 - - - -
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Residues in contact with CYS 678 (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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608B CYS* 3.0 2.1 - - - -
609B LYS* 2.8 41.8 + - + +
611B LYS* 5.0 9.2 - - - -
626B CYS* 2.0 55.0 - - + -
627B GLU 4.9 0.4 - - - +
630B TRP* 3.4 21.5 - - + -
631B THR 3.3 3.8 - - - -
676B ALA* 4.2 14.1 - - - -
677B ILE* 1.3 76.2 - - - +
679B CYS* 1.3 62.5 + - - +
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Residues in contact with CYS 679 (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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455B LEU* 3.9 12.1 - - + +
560B THR* 4.7 3.8 - - - -
606B LEU* 3.9 17.0 - - + -
607B GLU 2.9 7.0 - - - +
608B CYS* 2.0 46.7 - - - -
630B TRP* 3.7 4.3 - - - -
631B THR* 2.8 37.7 + - - +
633B THR* 3.6 25.1 - - - -
677B ILE* 4.4 2.2 - - - -
678B CYS* 1.3 75.9 - - - +
680B ARG* 1.3 60.5 + - - +
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Residues in contact with ARG 680 (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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455B LEU* 5.1 4.0 - - - -
606B LEU* 3.5 7.6 - - - +
607B GLU* 3.0 51.7 + - - +
629B GLY 3.6 22.6 - - - +
630B TRP* 3.2 50.7 - - + +
631B THR* 5.7 0.7 - - - -
679B CYS* 1.3 76.0 - - - +
681B SER* 1.3 74.5 + - - +
682B ARG* 5.9 0.8 - - + +
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Residues in contact with SER 681 (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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453B TRP* 3.4 49.5 + - - +
454B GLN* 4.3 4.7 - - - +
455B LEU* 5.0 4.2 - - - +
605B GLY 3.6 8.4 + - - -
606B LEU* 4.1 4.9 - - - +
680B ARG* 1.3 90.9 + - - +
682B ARG* 1.3 70.4 + - - +
683B HIS* 4.3 5.0 + - - +
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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