Contacts of the strand formed by residues 624 - 628 (chain A) in PDB entry 5IJ7
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 TRP 624 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A VAL* 3.7 23.8 - - + -
108A PRO* 2.9 40.9 + - + -
109A ILE 3.4 19.2 + - - -
110A MET* 3.6 22.4 - - + +
616A LEU* 3.6 21.3 - - + -
617A ALA 3.5 20.0 - - - -
618A PRO* 3.7 9.2 - - + -
619A SER* 3.8 2.2 - - - -
623A GLY* 1.3 74.3 - - - -
625A GLY* 1.3 52.7 + - - +
686A PHE* 3.7 19.0 - - + +
688A ASN* 2.8 26.5 + - - +
9001A 6BN 2.8 31.1 + - - +
566S PHE* 3.8 36.8 - + - -
571S CYS* 3.9 24.2 - - + -
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Residues in contact with GLY 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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616A LEU* 3.5 9.2 - - - +
617A ALA 2.9 35.1 + - - +
619A SER* 3.6 3.2 - - - +
624A TRP* 1.3 74.1 - - - +
626A ILE* 1.3 59.6 + - - -
627A PHE* 3.8 4.0 - - - -
686A PHE* 3.3 12.8 - - - -
688A ASN* 3.5 9.0 - - - -
721A GLU* 3.9 10.5 - - - -
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Residues in contact with ILE 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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614A LEU* 3.7 20.9 - - + -
615A LEU 3.3 21.8 - - - +
616A LEU* 4.1 6.7 - - + +
625A GLY* 1.3 71.8 - - - -
627A PHE* 1.3 60.0 + - - +
683A LYS* 3.5 40.2 - - + +
684A ILE* 4.3 5.6 - - + -
686A PHE* 3.3 17.7 + - + -
687A ALA* 3.6 34.2 - - + +
721A GLU* 3.4 5.9 - - - +
722A LEU* 2.8 49.5 + - + +
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Residues in contact with PHE 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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614A LEU* 3.4 5.2 - - - -
615A LEU* 2.7 47.3 + - - +
617A ALA* 3.4 38.8 - - + -
618A PRO 3.8 10.5 - - - -
619A SER* 4.4 0.2 - - - -
625A GLY 3.8 9.2 - - - -
626A ILE* 1.3 74.5 - - - +
628A ILE* 1.3 62.4 + - - +
719A GLY 3.4 24.0 - - - +
720A GLU 3.4 7.0 - - - +
721A GLU* 3.4 43.7 - - + -
722A LEU* 4.8 0.2 - - - -
563S ARG* 3.4 36.1 - - - -
565S TYR* 3.9 21.1 - + + +
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Residues in contact with ILE 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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612A LYS* 4.2 10.5 - - + -
613A HIS 4.0 6.7 - - - +
614A LEU* 3.9 11.4 - - + -
615A LEU* 4.9 1.5 - - - +
627A PHE* 1.3 70.9 - - - +
629A LYS* 1.3 58.3 + - - +
630A ASP 3.5 20.4 - - - +
632A VAL* 4.1 19.5 - - + -
638A ILE* 3.8 38.4 - - + -
716A ILE* 3.7 16.2 - - + +
717A GLN 3.4 23.3 - - - +
719A GLY* 2.9 30.5 + - - -
720A GLU 3.2 11.0 + - - +
722A LEU* 4.3 14.5 - - + +
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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