Contacts of the strand formed by residues 648 - 655 (chain I) in PDB entry 5G04
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 648 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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643I PHE* 3.8 0.6 - - - -
644I TYR* 2.9 36.5 + - - -
645I ASP* 2.7 41.6 + - - +
646I ASP 3.6 0.2 - - - -
647I GLU* 1.3 86.1 - - + +
649I VAL* 1.3 66.4 + - - +
668I GLN* 5.3 8.7 - - + -
669I LEU 3.4 7.6 - - - +
670I PRO* 3.8 21.8 - - + -
671I LEU* 4.6 0.7 - - - -
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Residues in contact with VAL 649 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587I LEU* 3.5 27.8 - - + -
598I MET* 4.1 16.4 - - + -
600I ILE* 5.5 0.9 - - + -
641I ALA* 4.2 1.1 - - + -
642I GLN 3.8 6.7 - - - +
643I PHE* 3.7 34.8 - - + -
644I TYR* 4.2 0.4 - - - +
648I THR* 1.3 78.3 - - - +
650I THR* 1.3 74.9 + - - +
651I VAL* 4.4 1.6 - - + -
668I GLN* 4.2 2.5 - - - -
669I LEU* 2.9 49.2 + - + +
671I LEU* 4.1 16.4 - - + -
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Residues in contact with THR 650 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641I ALA* 3.2 4.2 - - - -
642I GLN* 2.9 40.4 + - - -
644I TYR* 3.6 22.0 - - - +
648I THR 4.3 0.4 - - - -
649I VAL* 1.3 75.8 - - - +
651I VAL* 1.3 60.2 + - - +
666I LEU* 3.6 26.0 - - + -
667I VAL 3.7 0.4 - - - +
668I GLN* 3.1 24.5 + - - +
722I VAL* 4.1 20.0 - - + -
723I ALA 6.3 0.7 - - - -
724I GLY* 4.6 6.6 - - - -
731I SER* 5.3 4.0 - - - +
746I MET* 4.9 7.4 - - + -
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Residues in contact with VAL 651 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598I MET* 4.2 7.2 - - - -
620I PHE* 3.9 14.6 - - + -
638I CYS* 4.0 9.6 - - - -
640I ASP 3.4 13.7 - - - +
641I ALA* 4.3 0.4 - - + +
649I VAL* 3.6 13.7 - - + +
650I THR* 1.3 80.5 - - - +
652I VAL* 1.3 65.5 + - - +
653I LEU* 3.7 24.7 - - + -
665I LEU 3.8 0.3 - - - +
666I LEU* 3.5 8.6 - - - +
667I VAL* 2.9 47.7 + - + +
669I LEU* 3.9 24.2 - - + -
722I VAL* 4.6 1.3 - - - -
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Residues in contact with VAL 652 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638I CYS 3.7 1.2 - - - -
639I LEU* 2.8 49.5 + - + -
640I ASP* 2.9 22.1 + - + +
651I VAL* 1.3 75.2 - - - +
653I LEU* 1.3 63.9 + - - +
664I ARG* 5.4 2.0 - - + -
665I LEU 3.4 11.0 - - - +
666I LEU* 4.0 10.1 - - + -
714I LEU* 4.7 7.9 - - + -
719I ALA* 4.3 11.4 - - + +
720I GLN 3.8 18.4 - - - +
721I TYR 5.1 0.4 - - - -
722I VAL* 3.3 28.9 - - + +
733I VAL* 4.8 8.5 - - + -
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Residues in contact with LEU 653 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620I PHE* 3.6 41.5 - - + -
623I PHE* 3.5 35.4 - - + -
636I TYR* 4.1 16.2 - - + -
637I SER 3.3 12.8 - - - +
638I CYS* 4.0 7.0 - - - -
639I LEU* 4.3 3.4 - - - -
651I VAL* 3.7 16.8 - - + -
652I VAL* 1.3 77.7 - - - +
654I LYS* 1.3 61.3 + - - +
655I ASP 4.0 0.2 - - - -
664I ARG* 3.3 8.5 - - - +
665I LEU* 2.9 39.6 + - + +
667I VAL* 3.8 14.4 - - + -
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Residues in contact with LYS 654 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636I TYR* 3.5 3.6 - - - -
637I SER* 2.8 39.4 + - - +
639I LEU* 3.7 38.9 - - + +
653I LEU* 1.3 73.0 - - - +
655I ASP* 1.3 77.9 + - - +
656I THR* 3.2 8.4 + - - +
663I ASP* 3.6 13.9 - - - +
664I ARG* 4.1 23.0 - - + +
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Residues in contact with ASP 655 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632I ARG* 3.6 19.8 + - - -
634I SER* 2.9 24.3 + - - -
635I ILE 3.6 0.5 - - - +
636I TYR* 3.4 33.3 + - + -
653I LEU 4.0 1.2 - - - -
654I LYS* 1.3 83.2 - - - +
656I THR* 1.3 69.4 + - - +
657I VAL* 3.1 18.2 - - - +
658I GLY* 4.3 6.0 - - - +
662I ARG 5.3 1.9 - - - +
663I ASP* 2.7 36.6 + - - +
665I LEU* 4.4 4.9 - - + +
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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
------------------------------------------------------------
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