Contacts of the strand formed by residues 677 - 681 (chain D) in PDB entry 6T8B
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 ASP 677 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418D ARG* 3.6 16.8 - - - +
470D SER 4.9 0.5 - - - +
652D PHE* 3.2 23.6 - - - +
653D GLN* 3.8 2.9 + - - +
672D LEU* 3.7 13.0 - - + +
673D LEU* 3.4 10.5 + - - +
674D GLY* 3.6 16.7 + - - +
675D HIS 3.3 3.6 + - - -
676D GLY* 1.3 76.4 - - - +
678D MET* 1.3 73.7 + - - +
690D ARG* 2.4 42.4 + - - +
692D HIS* 3.2 23.6 + - - +
693D GLY 4.4 3.4 - - - +
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Residues in contact with MET 678 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443D LEU* 3.6 45.8 - - + -
475D GLY* 6.3 0.4 - - - -
479D MET* 5.7 1.1 - - - -
650D ILE* 3.4 26.5 - - + -
651D ALA 3.3 17.7 - - - +
652D PHE* 3.5 29.2 - - + -
672D LEU* 3.7 4.9 - - - -
676D GLY 4.4 1.1 - - - +
677D ASP* 1.3 83.9 + - - +
679D LEU* 1.3 55.6 + - - +
680D TYR* 5.2 2.5 - - + +
690D ARG* 3.8 1.0 - - - -
691D VAL* 2.7 69.0 + - + +
693D GLY* 4.3 12.3 - - - -
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Residues in contact with LEU 679 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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649D ARG 4.3 0.2 - - - +
650D ILE* 4.2 1.1 - - - -
651D ALA* 3.3 35.9 + - + +
664D LEU* 3.6 26.7 - - + +
666D GLN* 5.9 0.2 - - + -
668D GLY* 3.7 25.1 - - - +
669D ALA* 3.7 18.8 - - + -
672D LEU* 3.7 21.3 - - + -
678D MET* 1.3 76.6 - - - +
680D TYR* 1.3 62.4 + - - +
681D LEU 3.7 2.1 + - - -
688D PRO* 3.7 16.6 - - + +
689D ILE 3.3 10.8 - - - +
690D ARG* 3.9 9.4 - - + +
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Residues in contact with TYR 680 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443D LEU* 4.2 14.1 - - + -
452D ILE* 5.1 2.0 - - + -
454D THR* 3.7 25.1 + - + -
459D MET* 3.2 24.6 - - + +
648D THR* 3.3 27.8 - - + +
649D ARG 4.1 1.6 - - - -
650D ILE* 3.4 33.4 - - + -
678D MET* 4.1 4.1 + - + -
679D LEU* 1.3 67.0 - - - +
681D LEU* 1.3 59.6 + - - +
682D PRO* 3.3 22.9 - - + +
683D PRO* 3.3 11.6 - - + +
688D PRO* 3.5 2.1 - - - -
689D ILE* 2.4 82.9 + - + +
691D VAL* 4.1 15.2 - - + +
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Residues in contact with LEU 681 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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647D PRO 4.2 7.9 - - - +
648D THR* 3.5 5.5 - - - +
649D ARG* 3.1 63.2 + - + +
664D LEU* 4.2 33.9 - - + +
666D GLN* 5.1 5.6 - - + +
679D LEU 3.7 1.8 + - - -
680D TYR* 1.3 70.8 - - - +
682D PRO* 1.3 80.2 - - + +
684D GLY 5.1 2.5 - - - +
685D THR* 5.0 9.2 - - + -
686D GLY 3.7 26.7 - - - +
688D PRO* 4.0 18.6 - - + -
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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