Contacts of the strand formed by residues 513 - 519 (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 513 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15J PRO* 5.1 3.6 - - - +
98J PRO* 3.9 10.5 - - + +
99J ALA 3.1 22.9 - - - +
100J ALA* 3.6 20.2 - - + +
112J ILE* 4.8 7.2 - - + -
127J LEU* 4.4 1.8 - - + -
458J ALA* 3.4 20.2 - - + +
461J ILE* 3.9 18.4 - - + -
462J GLN* 3.6 34.5 + - + +
465J LEU* 3.5 31.0 - - + -
510J GLU 3.1 16.0 + - - +
511J TRP* 3.1 4.1 - - - +
512J MET* 1.3 76.6 - - + +
514J LEU* 1.3 60.6 + - - +
515J GLU* 3.9 1.9 + - - +
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Residues in contact with LEU 514 (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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1095I LEU 5.7 0.2 - - - -
1096I ALA* 3.7 17.9 - - + -
13J ALA 4.6 3.4 - - - +
15J PRO* 3.8 22.2 - - + -
18J ILE* 3.6 22.9 - - + -
95J LEU* 4.2 5.2 - - - +
98J PRO* 3.8 0.6 - - - +
99J ALA* 2.4 40.4 + - - +
100J ALA* 4.2 0.4 - - - +
101J HIS* 5.2 14.8 - - + +
511J TRP 4.3 10.3 - - - +
512J MET 3.6 4.1 + - - +
513J ILE* 1.3 72.2 - - - +
515J GLU* 1.3 69.5 + - - +
516J ALA 3.2 28.5 - - - +
517J VAL* 4.3 9.4 - - + +
518J PRO* 3.8 10.1 - - + -
578J VAL* 6.4 2.0 - - + -
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Residues in contact with GLU 515 (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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15J PRO* 4.0 15.0 - - + +
19J ARG* 3.9 20.1 + - - +
93J ILE 3.4 1.9 - - - +
94J GLU* 4.1 8.1 - - - +
95J LEU* 3.1 39.9 + - - +
98J PRO* 3.8 20.9 - - + +
462J GLN* 3.2 30.6 + - - +
513J ILE 3.9 2.0 + - - +
514J LEU* 1.3 77.9 - - - +
516J ALA* 1.3 64.3 + - - +
517J VAL 3.6 0.9 + - - -
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Residues in contact with ALA 516 (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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15J PRO* 4.1 20.1 - - + +
18J ILE* 3.2 31.5 - - + +
19J ARG* 4.2 3.1 - - - +
92J HIS* 4.0 13.2 - - + -
93J ILE 3.5 5.8 - - - -
94J GLU* 3.3 29.4 - - - +
514J LEU* 3.2 7.8 - - - +
515J GLU* 1.3 77.4 - - - +
517J VAL* 1.3 59.7 + - - +
518J PRO* 3.4 0.3 - - - +
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Residues in contact with VAL 517 (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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1094I ALA 5.3 1.6 - - - +
18J ILE* 4.2 0.4 - - - -
92J HIS* 3.2 3.5 - - - -
93J ILE* 2.9 46.6 + - + +
95J LEU* 3.7 33.2 - - + -
514J LEU* 4.3 11.4 - - + +
515J GLU 4.2 1.1 - - - +
516J ALA* 1.3 73.3 - - - +
518J PRO* 1.3 80.5 - - + +
519J VAL* 3.5 2.9 - - - +
544J TYR* 4.5 4.5 - - + -
547J LEU* 4.3 17.7 - - + -
578J VAL* 4.6 16.4 - - + -
581J VAL* 5.1 5.6 - - + -
582J ILE* 5.5 8.1 - - + -
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Residues in contact with PRO 518 (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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1093I GLN 3.3 26.9 - - - +
1094I ALA* 3.6 20.5 - - - +
1095I LEU 5.3 0.2 - - - -
1096I ALA* 3.9 5.4 - - + +
18J ILE* 3.6 30.7 - - + -
21J TRP* 4.8 4.7 - - + -
90J MET* 5.5 3.1 - - + -
91J GLY 3.6 8.3 - - - +
514J LEU* 3.8 12.3 - - + -
516J ALA 3.4 7.8 - - - +
517J VAL* 1.3 92.8 - - + +
519J VAL* 1.3 59.0 + - - +
544J TYR* 2.9 21.9 + - - -
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Residues in contact with VAL 519 (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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1094I ALA* 5.1 1.6 - - - -
26J VAL* 3.9 15.9 - - + -
44J LEU* 5.2 2.2 - - + -
50J PHE* 4.9 2.2 - - + -
90J MET* 3.2 10.5 - - - +
91J GLY* 2.9 37.9 + - - +
92J HIS 3.6 13.0 - - - +
93J ILE* 3.5 27.4 - - + -
517J VAL 3.5 11.7 - - - +
518J PRO* 1.3 77.0 - - - +
520J LEU* 1.3 65.4 + - - +
525J ARG* 3.8 25.4 - - - +
544J TYR* 3.5 20.6 - - + -
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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