Contacts of the strand formed by residues 627 - 635 (chain A) in PDB entry 2XRG
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 MET 627 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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621A TYR* 3.6 11.2 - - - -
622A SER* 3.1 25.9 + - - -
625A PHE* 3.6 23.8 - - + +
626A LEU* 1.3 79.0 - - - +
628A PRO* 1.4 78.4 - - + +
629A LEU* 5.2 0.5 - - - +
664A GLN* 3.6 11.4 - - - +
701A MET 4.3 2.7 - - - +
702A VAL* 4.3 5.6 - - + -
703A PRO* 3.8 26.5 - - + -
736A PRO* 4.0 23.1 - - + -
738A PHE* 4.3 11.0 - - + -
761A ILE* 4.3 7.0 - - + -
762A PRO* 3.4 33.2 - - + +
764A PRO* 4.5 2.2 - - + -
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Residues in contact with PRO 628 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619A SER* 4.2 9.6 - - - +
620A GLY 3.5 15.3 - - - +
621A TYR* 3.8 6.3 - - + -
627A MET* 1.4 92.9 - - + +
629A LEU* 1.3 60.9 + - - +
630A TRP 3.7 17.0 - - - +
631A THR* 4.2 4.3 - - - +
680A LEU* 3.6 25.1 - - + -
699A THR 3.4 26.0 - - - +
700A ASN* 5.1 4.5 - - - +
701A MET 4.7 1.8 - - - +
702A VAL* 4.6 5.4 - - + -
736A PRO* 3.3 25.6 - - - +
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Residues in contact with LEU 629 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603A VAL* 4.5 20.0 - - + -
605A TYR* 3.4 26.0 - - + +
607A THR* 5.3 4.0 - - + -
609A TYR* 4.4 16.8 - - + -
620A GLY 3.0 19.5 + - - +
622A SER* 3.9 27.4 - - - +
625A PHE* 5.0 8.7 - - + -
627A MET 5.2 0.2 - - - +
628A PRO* 1.3 73.7 - - - +
630A TRP* 1.4 61.6 + - + +
736A PRO* 3.9 14.6 - - + +
738A PHE* 6.6 0.2 - - + -
768A TYR* 2.9 27.5 + - - -
833A THR* 5.2 2.6 - - - +
835A LEU* 4.0 15.3 - - + +
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Residues in contact with TRP 630 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596A LEU* 3.9 30.3 - - + -
600A ARG* 4.6 5.8 - - + -
601A PRO* 3.6 41.6 + - + +
603A VAL* 5.4 0.4 - - - +
609A TYR* 5.0 7.4 - + - -
611A ILE* 4.2 16.8 - - + -
618A GLU* 3.7 26.0 - - - -
619A SER* 3.4 13.5 - - - -
620A GLY* 3.3 41.6 + - - -
628A PRO* 3.4 3.8 - - - +
629A LEU* 1.4 93.0 - - + +
631A THR* 1.4 70.5 + - - +
632A SER* 4.1 9.0 - - - -
680A LEU* 5.3 0.2 - - - -
733A ILE* 4.3 13.0 - - + -
734A SER 3.7 9.9 - - - -
735A GLY* 4.7 0.4 - - - -
768A TYR* 3.5 11.9 - - - +
835A LEU* 4.0 17.4 - - + +
837A PHE* 5.3 0.4 - - + -
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Residues in contact with THR 631 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617A PHE* 4.2 29.6 - - + -
618A GLU 3.4 11.2 - - - +
619A SER* 3.8 8.9 - - - -
628A PRO* 4.2 2.9 - - - +
630A TRP* 1.4 79.2 + - - +
632A SER* 1.4 60.9 + - - +
633A TYR* 4.4 9.6 - - + -
680A LEU* 3.6 29.1 - - + +
681A PHE* 4.5 13.5 - - + +
700A ASN* 4.7 2.7 + - - +
732A VAL 3.4 2.3 - - - +
733A ILE* 3.3 22.4 - - - -
734A SER* 3.2 17.0 + - - +
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Residues in contact with SER 632 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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595A HIS* 2.6 32.4 + - - +
596A LEU* 3.8 27.1 - - - +
617A PHE* 3.6 2.3 - - - -
618A GLU* 2.8 36.2 + - - -
630A TRP* 4.1 6.0 - - - -
631A THR* 1.4 73.5 - - - +
633A TYR* 1.4 63.3 + - - +
731A ASN* 4.1 4.2 + - - -
732A VAL 3.4 3.7 + - - -
733A ILE* 3.6 20.1 - - - +
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Residues in contact with TYR 633 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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595A HIS* 3.8 7.2 - - - -
616A ASP 3.5 21.1 - - - +
617A PHE* 4.3 0.4 - - + -
631A THR* 4.4 11.7 - - + -
632A SER* 1.4 79.6 + - - +
634A THR* 1.3 64.8 + - - +
635A ILE* 3.7 29.8 - - + -
680A LEU 4.1 15.7 + - - -
681A PHE* 3.6 26.7 - + + -
682A PRO* 3.6 23.8 - - + +
715A PHE* 5.2 3.8 - - - -
716A GLN* 4.7 3.3 + - - +
720A VAL* 4.9 10.2 - - + +
730A VAL 4.2 0.3 - - - +
731A ASN* 3.8 2.6 + - - -
732A VAL* 3.0 70.4 + - + +
734A SER* 4.4 6.8 + - - -
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Residues in contact with THR 634 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594A ARG* 2.9 59.7 + - - +
595A HIS* 3.6 15.7 + - - -
597A LEU* 3.9 14.2 - - + +
633A TYR* 1.3 73.9 - - - +
635A ILE* 1.4 68.9 + - - +
636A SER 4.3 0.2 - - - -
730A VAL 3.6 13.2 - - - +
731A ASN* 2.9 22.2 + - - -
781A ALA* 5.3 1.8 - - + -
782A ASP* 5.6 0.7 - - + -
1869A IOD 4.4 13.2 - - + -
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Residues in contact with ILE 635 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633A TYR* 3.7 32.0 + - + -
634A THR* 1.4 78.5 - - - +
636A SER* 1.3 71.9 + - - +
639A ALA* 4.2 14.4 - - + -
681A PHE* 5.4 1.8 - - + -
682A PRO* 5.2 0.2 - - + -
685A LEU* 3.7 49.8 - - + +
720A VAL* 3.8 15.5 - - + -
721A LYS* 4.6 5.2 - - + +
724A ALA* 3.7 15.4 - - + +
729A GLY* 3.4 1.1 - - - -
730A VAL* 3.0 35.6 + - + +
732A VAL* 5.6 1.3 - - + +
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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