Contacts of the strand formed by residues 713 - 721 (chain J) 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 ILE 713 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1032I PHE* 3.9 7.2 - - + -
1036I GLU* 3.7 35.2 - - + +
1039I ALA* 4.1 4.9 - - + -
1040I LEU* 3.7 26.2 - - + -
1043I TYR* 2.5 35.6 + - + -
701J LEU* 3.9 33.9 - - + -
702J LEU 3.2 9.2 - - - +
703J ASN* 3.2 26.9 - - + +
707J THR* 4.3 4.3 - - + -
710J ARG 3.0 6.2 + - - +
711J LEU 3.0 0.2 - - - -
712J GLY* 1.3 76.5 - - - +
714J GLN* 1.3 60.7 + - - +
763J MET* 4.5 4.6 - - - +
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Residues in contact with GLN 714 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1043I TYR* 3.8 8.1 - - - +
701J LEU* 4.4 3.8 - - - -
702J LEU 2.9 29.6 + - - +
711J LEU* 3.3 42.0 + - + +
713J ILE* 1.3 76.1 - - - +
715J ALA* 1.3 59.7 + - - +
716J PHE* 3.1 25.5 - - + -
732J VAL* 3.4 26.1 + - - +
735J ALA* 4.2 3.2 - - - +
736J PHE* 3.3 28.4 - - + -
763J MET* 3.7 5.2 - - - +
765J SER* 3.3 31.7 - - - +
768J ASN* 4.5 1.1 - - + +
778J LEU* 4.9 0.3 - - - +
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Residues in contact with ALA 715 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699J VAL* 3.7 15.7 - - + -
700J VAL 3.8 0.2 - - - -
701J LEU* 3.7 22.6 - - + +
714J GLN* 1.3 72.0 - - - +
716J PHE* 1.3 59.1 + - - +
759J ALA 3.4 20.6 - - - +
763J MET 2.7 23.2 + - - +
764J LEU* 3.3 13.1 - - + +
765J SER* 3.2 24.3 + - - -
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Residues in contact with PHE 716 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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639J LEU 3.2 21.5 - - - -
640J HIS 3.1 5.4 - - - -
641J GLN 3.2 20.4 - - - -
642J CYS* 3.5 25.1 - - + -
699J VAL* 3.6 5.1 - - - +
700J VAL* 2.9 37.7 + - - +
702J LEU* 3.9 10.5 - - + -
714J GLN* 3.1 44.2 - - + -
715J ALA* 1.3 74.2 - - - +
717J GLN* 1.3 62.4 + - - +
718J PRO* 3.2 1.2 - - - +
728J LEU* 3.6 15.7 - - + -
729J HIS* 4.5 2.7 - - + -
732J VAL* 3.5 30.3 - - + -
736J PHE* 4.0 12.1 - + - -
764J LEU* 5.0 0.2 - - - -
765J SER* 3.6 13.9 - - - -
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Residues in contact with GLN 717 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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640J HIS* 2.3 44.9 + - + +
641J GLN* 4.1 5.4 - - + -
642J CYS* 2.8 27.9 + - - +
695J ILE* 4.4 2.4 - - - +
696J HIS* 3.9 15.2 - - - +
697J GLY* 3.7 24.3 + - - +
698J LYS 3.5 15.7 + - - +
699J VAL* 3.4 24.7 - - + +
716J PHE* 1.3 65.1 - - - +
718J PRO* 1.3 82.9 + - - +
719J VAL* 3.4 8.4 + - + +
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Residues in contact with PRO 718 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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642J CYS* 3.8 9.6 - - - +
644J LEU* 3.7 22.4 - - + -
653J PHE* 4.5 8.3 - - + -
695J ILE* 4.0 22.8 - - + +
698J LYS 3.1 24.7 - - - +
699J VAL* 3.6 2.2 - - - -
700J VAL* 3.6 30.7 - - + -
716J PHE 3.2 7.1 - - - +
717J GLN* 1.3 98.2 + - - +
719J VAL* 1.3 62.1 + - - +
720J LEU 4.1 0.6 + - - -
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Residues in contact with VAL 719 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185H ARG* 5.9 3.1 - - - -
637J LEU* 5.1 6.5 - - + -
641J GLN* 4.3 20.6 - - + +
642J CYS 2.9 24.8 + - - +
643J GLY* 3.8 2.4 - - - -
644J LEU* 2.9 28.0 + - - +
692J GLU* 5.6 2.7 - - - +
717J GLN* 3.6 12.8 - - + +
718J PRO* 1.3 78.5 - - - +
720J LEU* 1.3 73.4 + - - +
721J VAL* 3.2 7.6 + - + +
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Residues in contact with LEU 720 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185H ARG* 3.2 35.4 - - - +
190H THR* 5.1 2.8 + - - -
644J LEU* 3.6 2.7 - - + +
646J LYS* 3.7 21.8 - - + -
649J ALA* 3.6 31.4 - - + -
688J TRP* 3.9 15.5 - - + +
691J LEU* 3.7 25.8 - - + -
692J GLU* 3.6 31.5 + - + +
695J ILE* 3.9 14.3 - - + +
718J PRO 4.1 1.6 + - - -
719J VAL* 1.3 79.2 - - - +
721J VAL* 1.3 59.7 - - - +
722J GLU* 5.6 0.4 - - - -
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Residues in contact with VAL 721 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190H THR* 5.3 10.1 - - + +
643J GLY* 4.1 6.3 - - - -
644J LEU 3.4 19.0 + - - +
645J PRO* 3.6 2.9 - - + +
646J LYS* 3.1 25.9 + - - +
719J VAL* 3.2 15.2 + - + +
720J LEU* 1.3 76.0 - - - +
722J GLU* 1.3 85.2 + - + +
725J SER 4.8 4.0 - - - +
727J GLN* 3.4 32.3 - - + +
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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