Contacts of the strand formed by residues 681 - 686 (chain B) in PDB entry 5TDE
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 681 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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629B ILE* 4.7 1.6 - - + +
631B PRO* 3.4 24.4 - - + +
649B SER 5.6 1.8 + - - +
650B LYS 5.6 1.6 + - - +
651B LEU* 4.1 10.0 - - + +
653B ARG* 4.1 1.6 - - - +
654B PRO* 3.3 8.5 - - - +
655B GLY 3.0 14.0 + - - -
657B VAL 3.3 6.1 - - - +
659B TYR* 3.9 17.5 - - + -
671B ASN* 3.7 34.1 - - - +
674B ILE* 3.8 17.9 - - + -
675B SER* 5.3 0.4 - - - +
680B GLY* 1.3 72.4 - - - -
682B TYR* 1.3 62.1 + - - +
683B GLU* 3.5 29.2 - - - +
684B GLY 3.9 3.1 - - - +
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Residues in contact with TYR 682 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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630B LYS* 3.6 38.3 + - - +
631B PRO* 3.4 15.0 - - - +
654B PRO* 4.1 21.2 - - + +
655B GLY 3.4 22.9 - - - +
656B SER 4.2 0.7 - - - -
657B VAL 2.7 24.0 + - - +
680B GLY 3.5 1.4 + - - -
681B VAL* 1.3 73.4 - - - +
683B GLU* 1.3 69.7 + - + +
707B THR* 3.5 30.4 - - + +
709B GLY* 3.9 25.1 + - - -
710B VAL* 3.5 19.7 - - + -
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Residues in contact with GLU 683 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492B LEU* 4.6 2.0 + - - +
493B PHE* 3.7 27.0 + - - -
629B ILE 3.5 13.7 - - - +
630B LYS* 4.0 20.5 + - + +
658B ALA* 3.2 5.4 - - + +
659B TYR 3.0 23.2 + - - -
681B VAL* 3.5 7.5 - - - +
682B TYR* 1.3 96.7 - - + +
684B GLY* 1.3 66.5 + - - +
685B VAL* 4.4 1.8 - - - +
703B ARG* 3.0 43.8 + - - -
704B TYR* 3.5 16.8 + - + +
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Residues in contact with GLY 684 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628B GLY* 3.3 2.4 - - - -
629B ILE 2.8 35.8 + - - +
659B TYR* 3.3 34.8 - - - -
681B VAL* 3.9 2.2 - - - +
683B GLU* 1.3 75.9 - - - +
685B VAL* 1.3 68.6 + - - +
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Residues in contact with VAL 685 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493B PHE* 5.7 2.2 - - + -
621B ILE* 4.0 19.7 - - + -
627B GLY 3.9 9.4 - - - +
628B GLY* 4.2 1.8 - - - -
659B TYR* 3.1 10.1 + - - -
660B VAL* 3.2 7.5 - - + +
661B SER 3.0 24.9 + - - +
667B SER* 4.6 3.6 - - - -
683B GLU* 4.4 6.7 - - - +
684B GLY* 1.3 79.5 - - - +
686B ALA* 1.3 72.0 + - - +
687B ILE* 4.1 3.4 - - + -
700B HIS* 3.8 33.0 - - + +
703B ARG* 3.6 20.6 - - - +
704B TYR* 3.5 14.8 - - - +
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Residues in contact with ALA 686 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621B ILE* 3.5 6.4 - - - +
625B THR* 2.6 33.1 + - - +
626B VAL* 4.4 2.5 - - + -
627B GLY 2.9 22.4 + - - +
628B GLY* 4.3 1.5 - - - +
661B SER 3.1 7.9 - - - +
662B ARG 4.0 5.4 - - - +
663B SER 4.0 11.0 - - - +
664B GLY* 4.3 7.0 - - - -
667B SER* 3.6 20.4 - - - +
685B VAL* 1.3 71.2 - - - +
687B ILE* 1.3 62.5 + - - +
688B GLY 3.2 0.2 - - - -
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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