Contacts of the strand formed by residues 624 - 629 (chain A) in PDB entry 6T8O
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 ILE 624 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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461A HIS* 3.7 3.5 - - - -
530A TRP* 6.5 0.9 - - + -
531A SER* 4.4 17.5 - - - +
534A GLU* 4.5 6.5 - - + -
535A MET* 4.0 34.1 - - + +
538A ARG* 3.6 19.3 - - - +
590A ILE* 3.3 16.6 - - + -
592A VAL* 4.3 13.7 - - + -
615A ILE* 4.4 15.9 - - + -
619A ALA* 3.2 32.9 + - + +
622A ALA* 4.3 1.8 - - + +
623A GLY* 1.3 87.4 - - - +
625A HIS* 1.3 64.7 + - - +
626A LEU* 4.2 18.4 - - + -
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Residues in contact with HIS 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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439A VAL* 5.5 1.3 - - + +
456A LEU* 3.7 26.7 - - + -
457A ALA* 4.3 19.5 + - + +
460A PRO* 3.0 32.8 - - + +
461A HIS* 3.8 6.5 - + - -
550A LEU* 5.2 3.8 - - + -
589A THR* 3.5 32.8 - - + +
590A ILE 2.4 15.8 + - - +
591A VAL* 4.1 6.7 - - + +
592A VAL* 2.5 37.0 + - - +
619A ALA 4.6 2.0 + - - -
620A ARG* 4.1 18.4 + - - +
623A GLY* 4.6 3.6 - - - -
624A ILE* 1.3 85.1 + - - +
626A LEU* 1.3 60.3 + - - +
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Residues in contact with LEU 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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456A LEU* 5.3 0.3 - - - +
461A HIS* 3.3 18.0 + - + +
462A LEU 3.3 25.6 + - - +
528A LEU* 5.5 4.5 - - + -
592A VAL* 3.3 23.6 - - + +
594A VAL* 5.4 1.1 - - + -
612A ILE* 3.8 30.5 - - + +
615A ILE* 3.7 30.7 - - + -
616A ALA* 6.1 2.2 - - + -
624A ILE* 4.2 7.0 - - + -
625A HIS* 1.3 85.2 - - - +
627A ILE* 1.3 65.3 + - - +
628A LEU* 3.7 36.6 - - + -
646A ILE* 5.9 2.2 - - + +
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Residues in contact with ILE 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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441A LEU* 5.4 0.4 - - + -
456A LEU* 3.7 24.7 - - + -
462A LEU* 3.6 32.8 - - + +
464A VAL* 4.5 14.4 - - + -
476A VAL* 5.0 12.6 - - + -
479A MET* 4.0 27.1 - - + -
480A LEU* 6.0 0.4 - - + -
591A VAL* 3.7 22.0 - - + -
592A VAL 2.9 9.2 + - - +
593A VAL* 3.4 18.3 - - + +
594A VAL 2.9 26.5 + - - +
626A LEU* 1.3 71.5 - - - +
628A LEU* 1.3 62.0 + - - +
629A ALA* 3.7 1.0 + - + +
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Residues in contact with LEU 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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462A LEU 3.0 8.8 + - - +
463A LEU* 3.4 29.4 - - + +
464A VAL* 2.6 37.2 + - - +
594A VAL* 3.8 28.0 - - + -
597A PHE* 3.8 26.0 - - + -
612A ILE* 4.2 18.2 - - + -
626A LEU* 3.7 34.5 - - + -
627A ILE* 1.3 72.5 - - - +
629A ALA* 1.3 54.8 + - - +
642A ILE* 4.4 4.3 - - + -
646A ILE* 3.9 17.3 - - + -
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Residues in contact with ALA 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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464A VAL* 3.3 21.1 - - + -
472A LYS* 4.6 6.5 - - + +
476A VAL* 4.4 17.5 - - + -
594A VAL 2.8 13.6 + - - +
595A ASP* 3.0 30.9 - - - +
596A GLU* 3.3 0.2 - - - -
597A PHE* 3.2 22.1 + - - -
627A ILE* 3.7 1.5 + - + +
628A LEU* 1.3 74.5 - - - +
630A THR* 1.3 60.8 + - - +
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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