Contacts of the strand formed by residues 713 - 717 (chain D) in PDB entry 6X34
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 SER 713 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686D TRP 3.5 12.8 - - - -
687D ALA* 3.9 17.0 - - - -
688D LEU 4.9 0.2 - - - -
692D TYR* 4.4 17.0 - - - -
707D VAL* 4.9 1.6 - - - -
708D GLY* 3.8 24.9 - - - +
710D ASP* 3.0 23.0 + - - +
712D TYR* 1.3 77.9 - - - +
714D TYR* 1.3 75.7 - - - +
722D TRP 5.0 0.3 - - - +
724D GLY 5.0 1.4 + - - -
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Residues in contact with TYR 714 (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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685D GLY* 3.4 0.5 - - - -
686D TRP* 2.7 46.0 + - + +
707D VAL* 5.8 0.4 - - - -
708D GLY* 4.4 4.0 - - - -
711D LEU* 3.3 27.5 + - + +
712D TYR 4.6 1.6 - - - -
713D SER* 1.3 79.3 - - - +
715D GLY* 1.3 55.4 + - - +
722D TRP 4.6 1.8 - - - -
723D THR* 4.9 8.7 - - - -
755D ILE* 5.5 9.0 - - + -
768D PHE* 3.6 34.5 - + + -
771D PHE* 4.0 19.9 - + + +
772D ASN 5.3 2.0 + - - -
777D PHE* 4.1 31.4 - + - -
1470D ARG* 4.7 6.8 - - - -
1471D ALA 4.2 4.5 + - - -
1472D VAL* 3.5 44.5 - - + +
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Residues in contact with GLY 715 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683D ARG* 5.8 2.9 - - - -
684D VAL 3.7 2.2 - - - -
685D GLY* 3.7 15.3 - - - -
707D VAL* 5.2 5.4 - - - -
708D GLY* 4.1 10.2 - - - -
714D TYR* 1.3 75.1 - - - +
716D PHE* 1.3 63.5 + - - +
721D LEU* 4.5 1.4 - - - +
722D TRP* 3.2 33.8 + - - +
768D PHE* 4.9 5.2 - - - -
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Residues in contact with PHE 716 (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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683D ARG* 5.3 1.7 - - - +
684D VAL* 3.2 25.6 + - - +
715D GLY* 1.3 75.8 - - - +
717D ASP* 1.3 67.4 + - - +
718D GLY 3.2 25.1 - - - -
719D LEU* 4.1 4.5 - - - -
720D HIS 3.5 36.8 - - - -
721D LEU* 3.6 17.9 - - + +
722D TRP* 4.9 2.0 - - - +
730D VAL* 5.0 5.2 - - + -
732D SER* 5.8 0.7 - - - -
744D VAL* 5.6 8.6 - - + +
757D PHE* 3.6 26.2 - - + -
759D ILE* 5.2 8.5 - - + -
764D VAL* 3.6 39.9 - - + -
766D GLY* 6.4 1.8 - - - -
768D PHE* 6.3 0.9 - - + -
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Residues in contact with ASP 717 (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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682D LEU 3.3 26.2 - - - +
683D ARG* 3.7 21.6 - - + +
684D VAL* 4.4 3.8 - - + +
716D PHE* 1.3 83.6 - - - +
718D GLY* 1.3 62.2 + - - +
719D LEU 3.8 0.7 + - - -
720D HIS* 3.5 14.5 + - - +
722D TRP* 4.7 6.5 + - - -
737D LEU* 4.7 1.8 - - - +
744D VAL* 5.9 4.5 - - - -
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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
------------------------------------------------------------
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