Contacts of the strand formed by residues 96 - 101 (chain A) in PDB entry 1UD8
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 ASN 96 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A THR* 2.8 16.7 + - - -
39A ALA* 3.8 5.7 - - + +
40A ILE* 2.8 26.5 + - - +
91A LYS* 5.7 0.4 - - - -
94A ASP 4.2 0.7 - - - -
95A ILE* 1.3 78.5 - - - +
97A VAL* 1.3 61.8 + - - +
98A TYR* 3.6 32.4 + - + -
226A ASP* 3.4 22.2 - - + +
358A TYR* 5.2 0.6 + - - -
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Residues in contact with VAL 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ILE 3.6 2.9 - - - +
42A ILE* 4.4 24.0 - - + -
87A ILE* 3.9 43.3 - - + -
90A LEU* 3.7 26.2 - - + -
91A LYS* 4.4 4.9 - - - -
95A ILE 3.9 7.4 - - - +
96A ASN* 1.3 76.3 - - - +
98A TYR* 1.3 63.2 + - - +
225A LEU* 3.8 16.8 - - + -
226A ASP* 2.8 44.6 + - - +
227A GLY 3.5 0.2 + - - -
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Residues in contact with TYR 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A MET* 3.6 33.0 - - + -
39A ALA* 3.7 15.5 - - + -
40A ILE 2.9 12.2 + - - +
41A TRP* 3.4 9.5 - - + -
42A ILE* 3.1 26.5 + - - +
96A ASN* 3.6 32.4 + - + -
97A VAL* 1.3 81.3 - - - +
99A GLY* 1.3 61.8 + - - +
226A ASP* 3.6 14.4 - - + -
227A GLY* 3.3 23.3 - - - +
228A TYR* 4.1 8.1 - - - +
229A ARG* 4.9 1.8 - - + +
257A PHE* 3.3 36.0 - + + +
259A VAL* 5.2 2.5 - - + -
358A TYR* 3.1 20.8 + - - -
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Residues in contact with GLY 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ILE* 3.9 16.6 - - - -
97A VAL 3.9 2.0 + - - -
98A TYR* 1.3 71.7 - - - +
100A ASP* 1.3 65.9 + - - -
101A VAL* 3.5 4.4 + - - +
219A PHE* 4.8 4.5 - - - -
225A LEU* 4.1 18.0 - - - +
227A GLY 3.0 10.3 + - - -
228A TYR* 3.2 7.8 - - - +
229A ARG* 2.9 22.0 + - - -
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Residues in contact with ASP 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A TYR* 3.4 1.6 + - - -
41A TRP* 3.2 13.1 + - - +
42A ILE* 3.3 22.9 + - - +
43A PRO 4.6 1.2 + - - -
44A PRO* 3.5 24.9 - - + +
45A ALA 5.1 0.3 + - - -
46A TYR* 2.8 21.6 + - - -
56A TYR* 2.7 29.4 + - - -
99A GLY* 1.3 73.1 - - - -
101A VAL* 1.3 67.4 + - - +
219A PHE* 4.3 4.1 - - - -
229A ARG* 3.0 36.0 + - - +
231A ASP* 3.8 6.8 - - - +
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Residues in contact with VAL 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A TYR* 3.4 1.6 - - - -
99A GLY 3.5 6.9 + - - +
100A ASP* 1.3 81.3 + - - +
102A VAL* 1.3 63.4 + - - +
103A MET* 3.6 36.3 + - + +
215A TRP* 3.8 25.8 - - + -
219A PHE* 3.9 15.3 - - + -
228A TYR* 4.2 15.3 - - + -
229A ARG 3.2 6.0 + - - +
230A LEU* 4.0 18.9 - - + +
231A ASP* 3.0 27.0 + - - +
244A TRP* 4.3 7.4 - - + -
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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