Contacts of the strand formed by residues 132 - 136 (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 ALA 132 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129I ILE 2.8 23.7 + - - +
130I ASN* 3.1 5.7 + - + +
131I GLY* 1.3 76.1 - - - +
133I ASP* 1.3 68.6 + - - +
134I ARG* 3.3 11.9 + - + +
394I PHE* 3.9 25.4 - - + -
632I ASN* 5.4 0.2 - - - +
707I ARG* 5.0 11.9 - - - +
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Residues in contact with ASP 133 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84I ARG* 3.9 23.1 + - - +
126I SER* 4.3 5.8 + - - +
127I PHE 3.2 15.9 - - - +
128I ILE* 3.5 23.5 - - + +
131I GLY 3.8 4.8 + - - -
132I ALA* 1.3 72.0 - - - +
134I ARG* 1.3 58.6 + - - +
394I PHE* 3.6 7.3 - - - -
395I LYS* 3.2 36.5 + - + +
397I GLU* 2.8 28.4 - - - +
632I ASN* 3.3 10.4 - - - +
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Residues in contact with ARG 134 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126I SER* 3.7 3.1 - - - -
127I PHE* 2.8 34.9 + - - +
129I ILE* 4.1 32.8 - - + +
132I ALA* 3.3 15.0 + - + +
133I ASP* 1.3 75.1 - - - +
135I VAL* 1.3 63.4 + - - +
386I PHE 4.5 6.3 - - - +
387I SER* 3.0 41.9 + - - +
392I SER* 4.4 7.3 + - - -
393I GLN* 3.1 27.0 - - - +
394I PHE* 3.9 19.1 - - + +
395I LYS* 3.9 4.7 - - - +
18S G 2.4 32.0 + - - -
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Residues in contact with VAL 135 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22I GLN* 4.1 6.7 - - - +
125I GLY 3.9 9.9 - - - +
127I PHE* 4.9 2.5 - - + +
134I ARG* 1.3 75.4 - - - +
136I ILE* 1.3 72.3 + - - +
137I VAL* 4.8 0.9 - - + -
392I SER* 3.1 3.4 - - - -
393I GLN* 2.9 51.7 + - - +
395I LYS* 4.3 7.9 - - + -
406I HIS* 3.5 31.0 - - + +
407I LYS* 3.7 43.3 - - + +
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Residues in contact with ILE 136 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22I GLN* 3.2 27.3 + - - +
127I PHE* 3.7 24.1 - - + -
134I ARG 5.9 0.2 - - - -
135I VAL* 1.3 81.1 - - - +
137I VAL* 1.3 70.9 + - - +
336I VAL* 3.5 25.7 - - + +
339I LEU* 4.2 13.5 - - + -
340I MET* 5.8 1.6 - - + -
385I PHE* 4.0 19.5 - - + -
386I PHE* 3.6 32.1 - - + -
391I LEU* 3.1 18.8 - - + +
392I SER* 4.1 11.4 - - - +
407I LYS* 5.1 0.3 - - - +
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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