Contacts of the strand formed by residues 91 - 100 (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 GLY 91 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18J ILE* 4.6 2.3 - - - +
21J TRP* 5.8 0.7 - - - +
22J SER* 3.3 14.0 - - - -
23J TYR* 4.4 1.6 - - - -
24J GLY 3.7 8.3 - - - -
26J VAL* 5.6 0.7 - - - -
50J PHE* 3.8 15.7 - - - -
90J MET* 1.3 77.5 - - - +
92J HIS* 1.3 63.1 + - - +
518J PRO* 3.6 3.8 - - - +
519J VAL* 2.9 35.3 + - - -
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Residues in contact with HIS 92 (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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18J ILE* 3.9 15.3 - - + -
19J ARG* 4.1 14.5 + - + +
22J SER* 2.5 33.8 + - - +
24J GLY* 3.3 5.6 + - - -
25J GLU* 3.2 48.3 - - + +
26J VAL* 3.5 5.0 + - - +
91J GLY* 1.3 75.9 - - - +
93J ILE* 1.3 64.8 + - - +
94J GLU* 3.2 35.5 + - + +
516J ALA* 4.0 7.2 - - + -
517J VAL 3.2 11.7 - - - +
519J VAL* 3.6 2.5 - - - +
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Residues in contact with ILE 93 (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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25J GLU* 4.0 5.4 - - - +
26J VAL* 4.1 7.6 - - + +
92J HIS* 1.3 77.2 - - - +
94J GLU* 1.3 64.1 + - - +
95J LEU* 3.4 15.9 + - + +
515J GLU 3.4 0.2 - - - +
516J ALA* 4.3 0.9 - - - -
517J VAL* 2.9 39.6 + - + +
519J VAL* 3.5 22.0 - - + -
544J TYR* 3.9 17.0 - - + -
547J LEU* 3.9 14.6 - - + -
548J ILE* 3.5 54.1 - - + -
551J ASN* 4.1 17.3 - - + +
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Residues in contact with GLU 94 (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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19J ARG* 3.0 42.1 + - - -
25J GLU* 2.9 27.6 + - - +
92J HIS* 3.2 31.8 + - - +
93J ILE* 1.3 69.7 - - - +
95J LEU* 1.3 64.7 + - - +
96J ALA 3.9 0.3 + - - -
515J GLU* 4.1 5.0 - - - +
516J ALA* 3.3 20.7 + - - +
551J ASN* 3.4 19.4 + - - +
555J LYS* 4.6 5.9 + - - +
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Residues in contact with LEU 95 (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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93J ILE* 3.4 26.2 - - + +
94J GLU* 1.3 77.4 + - - +
96J ALA* 1.3 66.9 + - - +
97J THR 3.7 11.9 - - - +
98J PRO* 4.5 5.0 - - + +
99J ALA* 3.7 23.1 - - + +
514J LEU 4.2 1.6 - - - +
515J GLU* 3.1 23.7 + - - +
517J VAL* 3.7 20.2 - - + -
547J LEU* 5.0 4.7 - - + -
551J ASN* 3.3 10.5 - - + +
574J LEU* 3.7 21.1 - - + -
578J VAL* 3.6 28.7 - - + -
159L ILE* 5.2 2.3 - - - +
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Residues in contact with ALA 96 (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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94J GLU 3.9 1.0 + - - -
95J LEU* 1.3 74.2 - - - +
97J THR* 1.3 58.8 + - - +
98J PRO* 3.5 8.1 - - - +
551J ASN* 3.4 7.3 + - - -
554J LEU* 3.7 16.9 - - + +
555J LYS* 3.6 28.1 - - + +
558J LEU* 4.0 17.9 - - + -
159L ILE* 3.5 39.7 - - - +
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Residues in contact with THR 97 (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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95J LEU* 3.7 5.4 - - - +
96J ALA* 1.3 75.3 - - - +
98J PRO* 1.3 76.5 + - - +
99J ALA* 3.3 3.5 + - - +
129J PHE* 4.4 13.9 - - + -
459J GLU* 4.3 13.4 + - - +
554J LEU* 3.6 23.8 - - + -
558J LEU* 5.6 2.5 - - + -
571J LYS* 3.6 37.6 - - + +
574J LEU* 3.6 19.2 - - + +
155L ARG* 6.1 0.7 - - - -
159L ILE* 5.4 2.0 - - - -
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Residues in contact with PRO 98 (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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95J LEU* 4.5 4.0 - - + +
96J ALA 3.5 9.9 - - - +
97J THR* 1.3 86.0 + - - +
99J ALA* 1.3 60.7 + - - +
458J ALA* 3.2 18.7 - - - +
459J GLU* 3.7 26.9 + - + +
462J GLN* 3.4 36.1 - - + +
513J ILE* 4.1 7.6 - - + -
514J LEU 3.8 6.7 - - - +
515J GLU* 3.8 24.0 - - + +
159L ILE* 5.1 3.6 - - + -
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Residues in contact with ALA 99 (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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95J LEU* 3.7 22.3 - - + +
97J THR 3.3 3.4 + - - +
98J PRO* 1.3 75.0 - - - +
100J ALA* 1.3 56.1 + - - +
458J ALA* 3.8 0.9 - - - -
513J ILE* 3.1 6.0 - - - +
514J LEU* 2.4 42.6 + - - +
574J LEU* 5.2 1.6 - - + -
575J GLN* 3.3 24.5 - - + +
578J VAL* 3.9 19.1 - - + -
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Residues in contact with ALA 100 (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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99J ALA* 1.3 77.1 - - - +
101J HIS* 1.3 63.1 + - - +
102J ILE 3.3 2.1 + - - -
105J VAL* 4.3 13.5 - - + -
112J ILE* 5.3 1.1 - - + -
127J LEU* 3.8 21.8 - - + -
458J ALA* 4.0 0.4 - - + +
512J MET 3.7 4.9 - - - +
513J ILE* 3.6 24.0 - - + +
514J LEU* 4.8 1.3 - - - -
575J GLN* 3.1 27.4 + - - +
578J VAL* 4.0 9.9 - - - +
579J ASP* 3.5 3.6 - - - +
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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