Contacts of the strand formed by residues 610 - 615 (chain I) in PDB entry 4XLN
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 ARG 610 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133G GLU* 4.4 4.4 + - - -
605I LYS* 3.1 34.9 - - - +
606I VAL 2.7 12.1 - - - +
607I ASP* 2.5 45.9 + - + +
609I THR* 1.3 75.9 - - - +
611I ILE* 1.3 61.5 + - - +
612I ALA* 3.5 2.8 + - + -
622I GLU* 3.7 33.8 + - - +
623I HIS 3.9 4.0 - - - +
624I PRO* 4.3 5.4 - - + -
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Residues in contact with ILE 611 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595I LEU* 5.7 1.3 - - + -
603I VAL* 4.9 0.2 - - + -
605I LYS 4.2 4.9 - - - +
606I VAL* 3.2 14.6 - - - +
609I THR 4.0 0.2 + - - -
610I ARG* 1.3 70.8 - - - +
612I ALA* 1.3 59.0 + - - +
613I VAL* 3.9 11.8 + - + -
622I GLU* 3.7 0.7 - - - -
623I HIS* 2.9 43.5 + - + +
625I LEU* 3.7 23.1 - - + -
641I PRO* 3.6 26.0 - - + -
643I VAL* 4.0 22.2 - - + -
655I LEU* 4.4 14.1 - - + -
656I ALA* 3.6 34.5 - - + +
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Residues in contact with ALA 612 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603I VAL* 3.7 0.5 - - - +
604I VAL* 2.8 36.2 + - + +
605I LYS* 2.9 56.5 + - + +
610I ARG 3.5 2.7 + - - +
611I ILE* 1.3 73.0 - - - +
613I VAL* 1.3 57.6 + - - +
620I LEU* 6.3 2.7 - - + -
622I GLU* 3.7 22.4 - - + +
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Residues in contact with VAL 613 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602I GLU 3.3 8.7 - - - +
603I VAL* 3.5 35.7 - - + +
604I VAL* 4.0 2.2 - - - +
611I ILE* 4.7 4.9 - - + +
612I ALA* 1.3 75.1 - - - +
614I ARG* 1.3 61.4 + - - +
615I TYR* 3.3 33.5 - - + +
620I LEU* 3.8 2.6 - - - +
621I VAL 2.9 44.2 + - - +
623I HIS* 3.9 12.6 - - + -
649I VAL* 4.9 4.5 - - + -
655I LEU* 4.4 18.6 - - + -
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Residues in contact with ARG 614 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601I GLY* 3.4 0.3 - - - -
602I GLU* 2.9 32.3 + - + +
604I VAL* 3.5 18.7 - - + +
613I VAL* 1.3 72.1 - - - +
615I TYR* 1.3 69.3 + - - +
618I GLY* 2.8 34.9 + - - +
619I ARG 4.2 0.4 - - - +
620I LEU* 3.3 48.5 - - + +
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Residues in contact with TYR 615 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597I ALA* 4.0 11.1 - - + -
598I GLU* 3.4 29.2 + - + +
599I GLU* 3.4 47.6 - - + -
600I ASP 3.8 1.3 - - - +
601I GLY* 3.6 13.0 - - - -
613I VAL* 3.3 30.2 - - + +
614I ARG* 1.3 80.7 - - - +
616I GLU* 1.3 66.4 + - - +
617I ASP* 3.2 21.8 - - - +
618I GLY* 3.0 15.5 + - - -
619I ARG* 3.4 6.2 + - - -
621I VAL* 3.7 28.9 - - + -
623I HIS* 2.8 25.5 + - - -
649I VAL* 5.5 1.1 - - + -
655I LEU* 4.4 0.7 - - - +
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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