Contacts of the strand formed by residues 28 - 32 (chain B) in PDB entry 1XDM
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 28 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B ILE 4.5 1.6 - - - -
23B VAL* 5.0 0.9 - - - -
27B LYS* 1.3 75.1 - - - +
29B ILE* 1.3 66.6 + - - -
72B SER 3.0 9.1 + - - -
73B ILE* 3.7 3.8 - - - -
74B GLY* 3.0 23.4 + - - -
75B GLY 3.5 4.2 + - - -
298B SER* 3.0 16.8 - - - -
299B PHE* 3.2 20.2 - - - -
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Residues in contact with ILE 29 (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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22B ILE* 3.2 37.0 - - + -
28B GLY* 1.3 74.2 - - - -
30B LEU* 1.3 63.3 + - - +
73B ILE* 4.9 0.7 - - - -
75B GLY 3.0 14.6 - - - +
77B ILE* 3.6 27.4 - - + -
144B PHE* 3.9 6.7 - - + -
185B ILE* 3.7 28.0 - - + -
227B LEU* 4.0 8.5 - - + -
268B CYS* 4.4 9.2 - - - -
299B PHE* 2.8 13.2 + - - +
300B SER* 3.2 23.3 - - - +
301B TYR 3.2 25.3 + - - +
305B LEU* 3.9 6.9 - - - +
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Residues in contact with LEU 30 (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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29B ILE* 1.3 73.3 - - - +
31B ALA* 1.3 62.4 + - - +
32B ALA* 3.5 7.8 + - + +
62B LEU* 4.9 5.8 - - + -
63B PHE* 4.1 13.5 - - + -
73B ILE* 4.2 9.7 - - + +
75B GLY 3.0 6.5 + - - -
76B VAL* 3.6 33.4 - - + -
77B ILE* 2.7 34.3 + - - +
301B TYR 3.5 8.5 - - - +
305B LEU* 4.0 19.7 - - + -
306B GLN* 3.9 31.0 - - + +
327B PHE* 3.6 27.6 - - + -
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Residues in contact with ALA 31 (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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30B LEU* 1.3 70.4 - - - +
32B ALA* 1.3 55.8 + - - +
33B ASP* 3.0 26.4 + - - +
34B GLU* 3.4 8.3 - - - +
77B ILE* 4.4 7.2 - - + -
146B LYS* 5.4 0.7 - - - +
229B LYS* 4.4 17.0 - - - +
300B SER 4.5 2.5 - - - +
301B TYR 2.8 25.9 + - - +
302B GLY* 3.9 6.5 - - - +
303B ARG* 4.8 5.8 - - - +
306B GLN* 3.1 16.7 + - - -
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Residues in contact with ALA 32 (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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30B LEU* 3.5 6.1 + - + -
31B ALA* 1.3 72.5 - - - +
33B ASP* 1.3 55.3 + - - +
34B GLU* 3.0 17.4 + - - +
59B ARG* 3.6 30.5 + - + +
62B LEU* 5.1 2.0 - - + -
63B PHE* 3.7 31.0 - - + -
76B VAL* 4.2 3.4 - - + -
77B ILE 3.3 19.2 + - - +
78B LEU* 4.3 2.0 - - + +
79B PHE 3.9 3.8 + - - -
306B GLN* 3.7 10.5 - - - +
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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