Contacts of the strand formed by residues 99 - 103 (chain B) in PDB entry 2XJZ
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 99 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97B TYR 3.7 0.4 + - - -
98B GLU* 1.3 74.6 - - - +
100B THR* 1.3 58.3 + - - +
109B HIS* 4.1 4.0 - - - -
110B LEU* 3.2 43.5 + - + +
52C LEU* 6.2 1.6 - - - -
67C LYS 4.8 1.6 - - - +
68C LEU* 3.6 31.2 - - + -
70C ARG* 3.6 46.0 - - + +
72C LEU* 5.0 5.8 - - + -
80C LEU* 4.3 8.5 - - + -
81C PHE* 3.6 23.1 - - + -
343J PRO* 3.9 11.0 - - + -
344J THR 3.8 5.2 - - - +
345J LEU* 4.4 9.2 - - + -
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Residues in contact with THR 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B ILE* 3.4 19.1 - - + +
98B GLU 3.3 12.6 + - - -
99B MET* 1.3 72.2 - - - +
101B MET* 1.4 67.5 + - - +
102B ARG* 4.1 7.2 - - + +
107B VAL* 3.0 36.8 - - + -
108B TYR 3.4 12.6 - - - +
110B LEU* 4.3 1.8 - - - +
343J PRO* 3.3 7.0 - - - +
344J THR* 2.7 45.6 + - + +
345J LEU 4.5 0.2 - - - -
346J MET* 3.4 12.8 - - - +
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Residues in contact with MET 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B THR* 1.4 70.1 - - - +
102B ARG* 1.3 65.4 + - - +
103B VAL* 4.6 0.9 - - - -
107B VAL* 3.7 0.2 - - - -
108B TYR* 2.9 42.8 + - + +
110B LEU* 3.8 23.6 - - + -
113B PHE* 3.6 50.9 - - + -
80C LEU* 5.6 3.8 - - + -
340J VAL* 4.4 10.8 - - + -
341J GLY* 3.4 28.5 - - - +
342J GLU 4.1 3.8 - - - +
343J PRO* 3.5 32.1 - - + -
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Residues in contact with ARG 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B THR* 4.1 2.8 + - + +
101B MET* 1.3 75.5 - - - +
103B VAL* 1.3 64.1 + - - +
104B LYS 4.2 4.3 - - - +
106B LYS 3.7 6.5 - - - +
107B VAL* 3.8 18.9 - - + +
128B TYR* 5.2 0.2 + - - -
342J GLU 6.0 0.2 + - - -
344J THR* 3.5 29.5 + - + +
345J LEU 2.9 28.7 + - - -
346J MET* 2.7 41.1 + - - +
348J GLY* 4.9 1.8 - - - +
349J GLU* 4.0 37.0 + - - +
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Residues in contact with VAL 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B MET* 4.4 3.4 - - + +
102B ARG* 1.3 80.3 - - - +
104B LYS* 1.3 68.5 + - - +
106B LYS* 3.0 27.3 + - - +
108B TYR* 4.4 16.4 - - + -
113B PHE* 3.6 28.3 - - + -
128B TYR* 3.3 34.1 - - + +
130B LEU* 3.7 22.4 - - + -
135B ILE* 4.7 0.2 - - + -
338J MET* 3.3 19.1 - - + -
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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