Contacts of the strand formed by residues 624 - 631 (chain C) in PDB entry 5NC5
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 THR 624 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576C VAL 3.3 8.1 + - - -
577C GLN* 3.5 22.1 + - - +
587C THR* 3.6 11.3 - - - +
613C ASN* 3.8 0.2 - - - +
614C GLY* 2.9 27.7 + - - +
616C GLY* 3.5 34.8 - - - +
617C PHE 4.1 1.9 + - - -
619C GLY 3.7 14.6 + - - +
620C ARG 4.8 0.9 - - - -
621C GLY 3.2 20.4 - - - +
622C GLN 3.3 0.6 + - - -
623C ASN* 1.3 82.1 - - - +
625C GLY* 1.3 62.4 + - - +
721C LEU* 6.1 0.7 - - - -
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Residues in contact with GLY 625 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575C MET* 4.0 1.7 - - - +
576C VAL* 2.8 36.8 + - - +
591C LEU* 4.4 9.6 - - - -
612C VAL 3.2 14.1 - - - -
614C GLY 4.2 0.4 - - - -
615C PHE 3.6 9.4 - - - -
616C GLY* 4.6 2.1 - - - -
624C THR* 1.3 78.4 + - - +
626C ILE* 1.3 62.6 + - - +
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Residues in contact with ILE 626 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573C MET* 3.9 12.8 - - + -
574C THR 3.5 13.5 - - - +
575C MET* 5.1 3.6 - - + -
576C VAL 4.9 0.2 - - - +
591C LEU* 4.3 5.0 - - - +
610C PHE 3.7 2.4 - - - +
611C ALA* 3.6 0.2 - - - -
612C VAL* 2.8 45.2 + - + -
615C PHE* 3.2 28.5 - - + +
616C GLY* 4.8 3.4 - - - -
617C PHE* 3.7 32.3 - - + +
625C GLY* 1.3 74.8 - - - +
627C ALA* 1.3 64.4 + - - +
628C PHE* 3.4 38.6 - - + -
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Residues in contact with ALA 627 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573C MET* 3.6 5.0 - - - +
574C THR* 2.8 54.1 + - + +
576C VAL* 5.4 0.4 - - + +
591C LEU* 4.5 7.9 - - + +
594C VAL* 4.2 16.8 - - + -
595C THR* 5.6 0.4 - - - +
598C TYR* 4.9 2.0 - - + -
609C VAL* 4.2 19.3 - - + -
610C PHE 3.6 3.6 - - - -
611C ALA* 4.2 5.8 - - + +
626C ILE* 1.3 74.5 - - - +
628C PHE* 1.3 61.6 + - - +
629C VAL* 3.9 1.4 + - + -
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Residues in contact with PHE 628 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C PHE* 4.2 20.9 - + - -
139C VAL* 3.8 21.3 - - + -
178C PHE* 4.2 19.3 - + - -
326C PRO 4.3 3.8 - - - +
327C TYR* 3.6 37.0 - + + -
572C PHE 4.1 2.7 - - - -
573C MET* 3.6 25.4 - - + -
608C SER 3.9 0.7 - - - +
609C VAL* 3.5 3.0 - - - -
610C PHE* 2.8 59.4 + + + +
612C VAL* 4.5 3.1 - - + -
615C PHE* 5.3 0.4 - + - -
626C ILE* 3.4 37.7 - - + -
627C ALA* 1.3 75.2 - - - +
629C VAL* 1.3 62.6 + - - +
630C SER 4.0 0.3 + - - -
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Residues in contact with VAL 629 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326C PRO 4.5 1.1 - - - -
327C TYR* 4.1 1.8 - - - -
571C VAL* 3.1 8.7 - - - +
572C PHE* 2.9 81.6 + - + +
574C THR* 4.1 5.4 - - - +
598C TYR* 4.1 22.4 - - + -
606C VAL* 3.8 26.5 - - + -
608C SER 3.6 10.3 - - - +
609C VAL* 4.7 5.8 - - + -
627C ALA 4.4 4.7 - - - +
628C PHE* 1.3 76.7 - - - +
630C SER* 1.3 66.0 + - - +
631C LEU* 4.4 0.2 - - + -
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Residues in contact with SER 630 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325C TYR 5.0 2.6 + - - -
326C PRO* 3.1 27.3 - - - -
327C TYR* 4.9 0.4 - - - -
328C ASP 5.8 0.2 + - - -
570C GLY 3.8 7.7 + - - -
571C VAL* 4.3 7.3 - - - +
606C VAL 3.8 1.2 - - - -
607C GLU* 3.0 25.3 + - - +
608C SER* 3.1 23.1 + - - +
628C PHE 4.0 0.4 + - - -
629C VAL* 1.3 78.4 - - - +
631C LEU* 1.3 68.8 + - - +
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Residues in contact with LEU 631 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570C GLY* 2.9 23.9 + - - +
571C VAL* 4.8 0.4 - - - -
572C PHE* 3.7 27.1 - - + -
605C ASN 3.3 15.5 - - - +
606C VAL* 3.9 18.4 - - + -
607C GLU* 3.8 8.9 - - - +
629C VAL* 4.4 0.9 - - + -
630C SER* 1.3 84.4 + - - +
632C LYS* 1.3 65.8 + - - +
637C ARG* 3.5 29.8 - - - +
644C VAL* 3.4 33.2 - - + -
647C ILE* 3.9 16.8 - - + -
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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