Contacts of the strand formed by residues 639 - 644 (chain C) in PDB entry 1T9D
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 639 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570C VAL 3.2 4.3 + - - +
571C LYS* 3.3 29.7 - - + +
572C ILE* 2.8 27.7 + - - +
614C LEU* 4.1 5.3 - - - +
615C LYS* 3.4 25.4 - - + +
617C LEU* 4.1 15.3 - - + -
632C PHE* 3.5 31.4 - - + +
635C THR* 3.9 18.2 - - + +
638C PRO* 1.3 76.7 - - - +
640C LEU* 1.3 68.7 + - - +
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Residues in contact with LEU 640 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553C PHE* 3.6 31.4 - - + -
560C LEU* 4.7 8.3 - - + -
572C ILE* 3.3 19.1 - - + +
574C ILE* 3.8 22.0 - - + -
605C PHE* 4.1 30.5 - - + +
606C ILE* 4.7 2.0 - - + -
609C ALA* 4.0 19.3 - - + -
614C LEU* 4.8 4.2 - - + +
615C LYS 2.9 7.4 + - - +
616C GLY* 3.6 0.5 - - - -
617C LEU* 2.8 31.0 + - - +
639C VAL* 1.3 77.7 - - - +
641C LEU* 1.3 72.4 + - - +
642C GLU* 4.0 4.3 - - + +
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Residues in contact with LEU 641 (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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572C ILE 2.7 8.7 + - - +
573C LEU* 3.3 20.5 - - + +
574C ILE 2.8 25.3 + - - -
617C LEU* 3.3 22.0 - - + +
619C VAL* 3.4 30.7 - - + -
628C LYS* 4.2 6.1 - - + +
629C LEU* 3.8 21.8 - - + +
632C PHE* 3.4 50.4 - - + -
640C LEU* 1.3 74.7 - - - +
642C GLU* 1.3 62.8 + - - +
643C VAL* 3.9 5.4 - - + -
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Residues in contact with GLU 642 (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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574C ILE* 3.6 9.9 - - + +
576C ASN* 2.9 38.1 + - + +
605C PHE* 3.7 23.1 + - + -
606C ILE* 3.6 16.9 - - + +
617C LEU 2.7 9.7 + - - -
618C ARG* 2.9 37.8 + - - +
619C VAL 2.8 26.2 + - - -
640C LEU* 4.0 7.3 - - + +
641C LEU* 1.3 71.8 - - - +
643C VAL* 1.3 62.1 + - - +
644C GLU* 3.6 17.5 - - - +
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Residues in contact with VAL 643 (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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471C ILE* 3.9 26.0 - - + -
476C VAL* 4.0 23.8 - - + -
573C LEU* 3.7 26.2 - - + -
574C ILE 2.9 9.4 + - - +
575C LEU* 4.6 4.9 - - + -
576C ASN* 2.9 25.7 + - - -
619C VAL* 3.7 9.2 - - + +
625C LEU* 4.2 10.5 - - + -
641C LEU* 3.9 15.7 - - + -
642C GLU* 1.3 78.3 - - - +
644C GLU* 1.3 62.9 + - - +
645C VAL* 3.3 11.6 + - + +
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Residues in contact with GLU 644 (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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470C LYS* 5.0 17.0 + - - +
471C ILE* 3.7 24.1 + - - +
576C ASN* 3.7 11.0 - - + +
618C ARG* 3.7 10.0 + - + -
619C VAL 3.0 14.2 + - - +
620C LYS* 3.1 52.6 + - - +
642C GLU* 3.6 19.0 - - - +
643C VAL* 1.3 72.0 - - - +
645C VAL* 1.3 61.4 + - - +
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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