Contacts of the strand formed by residues 621 - 626 (chain A) in PDB entry 3ZFM
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 621 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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616A ILE* 3.9 11.2 - - + -
617A ASP 4.2 4.5 - - - +
618A ILE* 3.1 19.0 + - + +
619A SER* 4.2 4.4 - - - +
620A CYS* 1.4 81.4 - - - +
622A LYS* 1.3 65.7 + - - +
623A ILE* 4.7 6.2 - - + +
639A HIS 3.7 3.6 - - - +
640A LEU* 3.8 17.3 - - + -
650A VAL* 6.0 0.2 - - + -
652A ILE* 3.8 28.5 - - + -
689A VAL* 4.4 2.7 - - + -
696A MET* 4.0 30.1 - - + -
698A ILE* 3.9 18.2 - - + -
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Residues in contact with LYS 622 (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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620A CYS 5.4 0.7 - - - +
621A VAL* 1.3 76.8 - - - +
623A ILE* 1.4 64.5 + - - +
624A GLU 3.5 0.2 + - - -
638A GLY* 3.3 3.2 - - - -
639A HIS* 3.0 49.6 + - + +
647A GLU* 5.4 3.4 - - - +
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Residues in contact with ILE 623 (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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621A VAL* 4.7 7.0 - - + -
622A LYS* 1.4 69.5 - - - +
624A GLU* 1.3 62.6 + - - +
625A GLN 4.5 5.4 - - - +
636A CYS* 4.1 23.8 - - + -
637A SER 3.8 12.3 - - - +
638A GLY* 4.4 0.9 - - - -
652A ILE* 4.5 13.5 - - + -
654A THR* 5.9 5.4 - - + -
694A PRO* 6.2 5.2 - - + -
696A MET* 4.8 16.4 - - + -
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Residues in contact with GLU 624 (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 LYS 3.5 0.6 + - - -
623A ILE* 1.3 74.9 - - - +
625A GLN* 1.4 65.9 + - + +
637A SER* 3.0 15.3 + - - +
638A GLY* 4.3 9.0 - - - -
639A HIS* 4.4 18.8 - - + +
649A PHE* 5.4 3.8 - - + -
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Residues in contact with GLN 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 ILE* 4.5 3.6 - - - +
624A GLU* 1.4 81.0 - - + +
626A VAL* 1.3 72.2 + - + +
627A ILE* 6.1 4.0 - - + -
636A CYS* 3.5 7.1 - - - +
637A SER* 2.8 42.3 + - - +
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Residues in contact with VAL 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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625A GLN* 1.3 87.0 - - + +
627A ILE* 1.3 67.0 + - - +
634A GLU* 4.8 10.1 - - + -
635A VAL* 3.3 22.0 - - + +
636A CYS* 4.1 14.4 - - - -
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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