Contacts of the helix formed by residues 624 - 634 (chain A) in PDB entry 1JPP
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 ASP 624 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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584A VAL* 5.5 3.0 - - - +
587A ARG* 3.7 28.0 + - - +
621A LEU 3.5 8.3 + - - +
622A ALA 2.9 5.0 - - - -
623A GLN* 1.3 89.6 - - - +
625A LYS* 1.3 67.9 + - - +
626A GLU* 3.4 2.2 - - + +
627A ALA* 2.8 22.7 + - + +
628A ALA* 2.9 11.1 + - - -
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Residues in contact with LYS 625 (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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623A GLN 4.3 0.4 - - - -
624A ASP* 1.3 68.6 - - - +
626A GLU* 1.3 68.7 + - + +
628A ALA* 3.1 7.3 + - - +
629A GLU* 3.0 45.4 + - + +
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Residues in contact with GLU 626 (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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591A ARG* 5.0 12.1 + - - +
624A ASP* 3.1 2.7 + - + -
625A LYS* 1.3 80.4 - - + +
627A ALA* 1.3 64.0 + - - +
629A GLU* 3.2 12.0 + - - +
630A ALA* 3.1 22.6 + - - +
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Residues in contact with ALA 627 (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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591A ARG* 5.1 18.1 - - + +
596A ILE* 4.4 4.4 - - + +
621A LEU* 3.0 33.9 - - + +
624A ASP* 2.8 18.8 + - + +
626A GLU* 1.3 75.5 - - - +
628A ALA* 1.3 64.2 + - - +
630A ALA* 3.1 9.0 + - - +
631A ILE* 3.1 26.8 + - + +
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Residues in contact with ALA 628 (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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622A ALA* 3.6 23.7 - - - +
624A ASP 2.9 8.0 + - - +
625A LYS* 3.5 10.5 - - - +
627A ALA* 1.3 74.8 - - - +
629A GLU* 1.3 65.2 + - + +
631A ILE* 3.0 23.2 + - - +
632A GLU* 3.0 14.4 + - - +
661A ARG 4.7 2.9 - - - +
662A MET* 4.0 29.4 - - + +
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Residues in contact with GLU 629 (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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625A LYS* 3.0 46.9 + - + +
626A GLU* 3.5 12.1 + - - +
628A ALA* 1.3 78.4 - - + +
630A ALA* 1.3 61.0 + - - +
632A GLU* 3.4 8.5 + - - +
633A ALA* 3.1 23.4 + - - +
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Residues in contact with ALA 630 (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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591A ARG* 4.1 20.0 - - - +
596A ILE* 4.2 14.6 - - + +
626A GLU 3.1 13.1 + - - +
627A ALA 3.1 8.9 + - - +
629A GLU* 1.3 77.6 - - - +
631A ILE* 1.3 62.5 + - - +
633A ALA* 3.5 15.3 + - - +
634A GLU* 3.5 17.8 + - - +
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Residues in contact with ILE 631 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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596A ILE* 3.9 26.2 - - + -
600A VAL* 4.7 4.7 - - + -
618A LEU* 4.1 34.5 - - + +
621A LEU* 4.9 4.9 - - + -
622A ALA* 4.0 31.2 - - + +
627A ALA 3.1 16.6 + - - +
628A ALA* 3.0 7.7 + - - +
630A ALA* 1.3 74.8 - - - +
632A GLU* 1.3 64.7 + - - +
634A GLU* 3.1 17.7 + - - +
635A GLY 3.6 4.0 + - - -
636A ALA* 3.9 24.6 + - + +
658A VAL* 5.0 3.4 - - + -
662A MET* 4.3 13.5 - - + -
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Residues in contact with GLU 632 (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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628A ALA 3.0 9.8 + - - +
629A GLU* 3.8 9.7 - - - +
631A ILE* 1.3 77.3 - - - +
633A ALA* 1.3 60.0 + - - +
634A GLU 3.3 0.2 - - - -
635A GLY* 3.4 12.7 + - - +
636A ALA 4.9 3.6 - - - +
637A THR* 4.0 19.4 + - - +
662A MET* 3.6 39.4 - - - +
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Residues in contact with ALA 633 (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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629A GLU 3.1 17.1 + - - +
630A ALA* 3.6 11.7 - - - +
631A ILE 3.1 0.4 - - - -
632A GLU* 1.3 76.5 - - - +
634A GLU* 1.3 65.0 + - + +
635A GLY 3.6 0.2 + - - -
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Residues in contact with GLU 634 (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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596A ILE* 4.2 18.2 - - + -
597A PRO* 3.9 32.3 - - + +
600A VAL* 4.2 18.5 - - + +
630A ALA 3.5 14.2 + - - +
631A ILE 3.1 8.1 + - - +
633A ALA* 1.3 80.6 - - - +
635A GLY* 1.3 59.6 + - - +
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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