Contacts of the helix formed by residues 677 - 694 (chain A) in PDB entry 2PZI
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 ARG 677 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425A ASP* 3.4 32.3 + - - +
428A VAL* 3.8 28.3 + - - +
429A ALA* 3.9 13.3 - - - +
432A ASP* 2.9 36.8 + - - +
638A THR* 5.3 4.4 + - - -
641A LEU* 3.8 15.3 - - + -
675A GLU 3.5 0.4 + - - -
676A PRO* 1.3 79.4 - - + +
678A VAL* 1.3 63.3 + - - +
679A LEU* 3.4 2.6 - - - +
680A GLN* 3.2 34.0 + - - +
681A ILE* 3.1 24.6 - - + +
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Residues in contact with VAL 678 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641A LEU* 4.3 16.6 - - + -
668A VAL* 4.3 5.5 - - + +
671A LEU* 3.8 29.4 - - + +
672A PRO 3.5 25.4 - - - +
673A PRO* 4.2 8.5 - - + -
675A GLU* 3.3 32.5 + - + +
676A PRO 3.3 1.8 - - - +
677A ARG* 1.3 78.8 - - - +
679A LEU* 1.3 60.2 + - - +
681A ILE* 3.2 2.6 + - - +
682A ARG* 2.9 48.4 + - + +
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Residues in contact with LEU 679 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673A PRO* 5.7 5.5 + - + +
675A GLU 4.9 0.4 + - - -
677A ARG* 3.4 1.0 - - - +
678A VAL* 1.3 82.7 - - - +
680A GLN* 1.3 57.2 + - - +
682A ARG* 3.4 13.9 - - + +
683A ALA* 3.1 25.8 + - - +
720A SER* 3.6 26.0 - - - +
723A SER* 3.2 33.2 - - - +
724A LEU* 3.6 34.0 - - + +
727A VAL* 4.1 11.4 - - + -
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Residues in contact with GLN 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A VAL 3.6 2.2 + - - -
431A THR* 2.6 41.7 + - - +
432A ASP* 3.1 29.8 + - - +
434A TYR* 3.7 28.2 - - + -
435A LEU* 4.3 17.8 - - - +
677A ARG* 3.2 35.0 + - - +
679A LEU* 1.3 78.6 - - - +
681A ILE* 1.3 58.3 - - + +
683A ALA* 3.4 7.6 - - - +
684A LEU* 2.9 24.6 + - - +
724A LEU* 4.2 12.1 - - + -
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Residues in contact with ILE 681 (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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428A VAL* 5.0 3.1 - - + -
431A THR* 3.3 35.0 - - + +
641A LEU* 3.8 28.0 - - + +
644A ALA* 3.8 17.5 - - + -
645A VAL* 3.7 23.1 - - + -
668A VAL* 3.8 22.7 - - + -
677A ARG* 3.1 20.9 - - + +
678A VAL 3.2 2.1 + - - +
680A GLN* 1.3 75.5 - - + +
682A ARG* 1.3 57.1 + - - +
684A LEU* 3.5 8.4 - - + +
685A VAL* 2.7 35.1 + - + +
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Residues in contact with ARG 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668A VAL* 3.6 17.6 + - + +
669A GLU* 4.8 11.9 + - - +
671A LEU 5.7 2.2 + - - -
673A PRO* 6.3 1.3 - - - -
678A VAL* 2.9 29.3 + - - +
679A LEU* 3.4 17.7 - - + +
681A ILE* 1.3 74.3 - - - +
683A ALA* 1.3 63.3 + - - +
685A VAL* 3.1 2.8 + - - +
686A LEU* 2.9 32.8 + - + +
704A LEU* 2.8 62.9 + - + +
706A PHE* 4.3 14.3 - - - -
720A SER* 4.5 9.2 + - - +
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Residues in contact with ALA 683 (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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434A TYR* 4.0 18.5 + - + -
679A LEU 3.1 10.4 + - - +
680A GLN 3.4 11.4 - - - +
682A ARG* 1.3 78.6 - - - +
684A LEU* 1.3 56.3 + - - +
686A LEU* 3.8 3.3 - - - +
687A GLY* 2.8 28.6 + - - -
717A VAL* 4.6 7.5 - - + +
720A SER* 3.8 25.9 + - - -
721A LEU* 5.2 4.0 - - + -
724A LEU* 4.1 10.5 - - + -
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Residues in contact with LEU 684 (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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431A THR* 3.7 30.3 - - + -
434A TYR* 3.8 28.9 + - + +
644A ALA 5.3 0.2 - - - -
645A VAL* 4.6 22.4 - - + +
648A LEU* 4.0 25.7 - - + +
680A GLN 2.9 16.9 + - - +
681A ILE* 3.2 10.3 + - + +
683A ALA* 1.3 75.4 - - - +
685A VAL* 1.3 60.9 + - + +
687A GLY* 3.5 1.9 + - - -
688A GLY* 2.9 24.6 + - - -
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Residues in contact with VAL 685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644A ALA* 4.1 14.8 - - + -
648A LEU* 4.2 19.3 - - + +
661A ILE* 4.6 7.3 - - + +
664A ALA* 4.2 5.8 - - + +
665A ALA* 4.0 25.1 - - + +
668A VAL* 3.7 20.9 - - + -
681A ILE* 2.7 23.7 + - + +
682A ARG 3.7 2.9 - - - +
684A LEU* 1.3 71.5 - - + +
686A LEU* 1.3 61.6 + - - +
688A GLY* 3.1 3.8 + - - -
689A ALA* 3.0 26.9 + - - +
703A ILE* 4.2 7.0 - - + -
704A LEU* 3.9 19.3 - - + -
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Residues in contact with LEU 686 (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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682A ARG* 2.9 22.9 + - + +
683A ALA 3.9 2.0 - - - +
685A VAL* 1.3 75.3 - - - +
687A GLY* 1.3 63.5 + - - +
689A ALA* 3.3 5.8 + - - +
690A LEU* 2.9 23.4 + - - +
703A ILE* 3.5 35.9 - - + +
704A LEU* 3.9 15.7 - - + -
706A PHE* 4.1 22.9 - - + -
713A LEU* 3.9 19.5 - - + +
716A GLY* 4.0 14.8 - - - +
717A VAL* 3.7 17.1 - - + +
720A SER* 3.8 20.0 - - - +
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Residues in contact with GLY 687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A TYR* 6.0 0.7 - - - -
683A ALA 2.8 21.4 + - - -
684A LEU* 3.6 2.7 - - - -
686A LEU* 1.3 72.5 - - - +
688A GLY* 1.3 60.8 + - - +
690A LEU* 3.2 7.2 + - - +
691A ASP* 3.1 30.7 + - - +
717A VAL* 3.6 13.5 - - - +
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Residues in contact with GLY 688 (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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648A LEU* 5.0 15.7 - - - -
661A ILE* 4.7 7.0 - - - +
684A LEU 2.9 17.8 + - - -
685A VAL 3.1 4.4 + - - -
687A GLY* 1.3 71.2 - - - +
689A ALA* 1.3 56.3 + - - +
691A ASP* 3.4 10.4 + - - +
692A TRP* 3.1 27.5 + - - +
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Residues in contact with ALA 689 (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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661A ILE* 3.9 27.0 - - + +
685A VAL 3.0 14.9 + - - +
686A LEU* 3.7 5.8 - - - +
688A GLY* 1.3 73.4 - - - +
690A LEU* 1.3 64.1 + - - +
692A TRP* 3.5 8.7 - - - +
693A LEU* 3.3 18.0 + - - +
703A ILE* 4.4 8.7 - - + -
708A PHE* 4.3 5.5 - - + -
713A LEU* 3.2 31.0 - - + +
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Residues in contact with LEU 690 (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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686A LEU 2.9 13.2 + - - +
687A GLY* 3.2 10.5 + - - +
689A ALA* 1.3 73.2 - - - +
691A ASP* 1.3 80.2 + - - +
692A TRP 3.1 2.1 + - - -
693A LEU* 3.2 12.9 + - - +
694A LYS* 3.6 28.2 + - - +
710A SER* 5.0 6.1 + - - +
713A LEU* 3.6 15.6 - - + +
714A ARG* 3.3 51.4 - - + +
717A VAL* 4.3 5.6 - - + -
744A VAL* 4.0 15.0 - - + -
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Residues in contact with ASP 691 (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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687A GLY* 3.1 19.1 + - - +
688A GLY* 3.8 9.2 - - - +
690A LEU* 1.3 81.7 - - - +
692A TRP* 1.3 61.3 + - - +
694A LYS* 2.9 46.9 + - + +
695A ASP* 4.4 4.2 + - - +
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Residues in contact with TRP 692 (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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656A VAL* 3.4 26.3 + - + -
657A THR* 3.9 3.4 - - - +
658A GLU* 3.3 37.9 - - + -
661A ILE* 3.7 20.4 - - + -
688A GLY 3.1 17.2 + - - +
689A ALA* 3.5 8.5 - - - +
690A LEU 3.1 0.2 - - - -
691A ASP* 1.3 74.8 - - - +
693A LEU* 1.3 64.9 + - + +
694A LYS 3.0 4.7 - - - -
695A ASP* 3.0 19.6 + - - +
696A ASN* 3.2 50.8 + - + +
697A LYS 3.3 32.1 - - - -
698A ALA 4.1 0.4 - - - -
708A PHE* 3.8 31.9 - + - -
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Residues in contact with LEU 693 (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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689A ALA 3.3 5.8 + - - +
690A LEU* 3.2 10.1 + - - +
692A TRP* 1.3 83.1 - - + +
694A LYS* 1.3 62.9 + - - +
695A ASP 3.2 0.2 - - - -
696A ASN 3.3 27.7 + - - +
697A LYS* 4.5 0.2 - - - -
698A ALA* 4.0 15.7 - - + +
708A PHE* 3.7 30.5 - - + +
709A THR* 3.5 13.5 - - - -
710A SER* 3.3 41.7 + - - +
713A LEU* 3.6 11.4 - - + -
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Residues in contact with LYS 694 (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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690A LEU* 3.6 23.2 + - - +
691A ASP* 2.9 44.6 + - + +
692A TRP 3.0 0.4 + - - -
693A LEU* 1.3 80.1 - - - +
695A ASP* 1.3 70.2 + - - +
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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
------------------------------------------------------------
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