Contacts of the strand formed by residues 96 - 102 (chain D) in PDB entry 2QXU
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 VAL 96 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70D LYS* 2.8 22.0 + - - +
71D VAL* 3.4 11.2 - - + +
73D ILE* 3.8 26.7 - - + -
86D TYR* 3.8 17.5 - - + -
87D ILE* 4.4 6.1 - - + -
92D GLY 3.4 16.0 + - - +
93D GLY 5.0 0.2 - - - +
94D ASN* 4.7 0.2 - - - +
95D LYS* 1.3 84.4 - - - +
97D ALA* 1.3 60.9 + - - +
98D ASN 4.1 6.5 - - - +
99D VAL* 3.4 32.1 - - + -
123D ILE* 3.4 27.0 - - + +
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Residues in contact with ALA 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D ASN* 3.4 18.2 - - - +
70D LYS* 3.7 19.9 - - + +
71D VAL 3.0 7.8 + - - +
72D ASP* 3.3 13.0 - - - +
96D VAL* 1.3 73.9 - - - +
98D ASN* 1.3 71.7 + - - +
121D GLN* 4.1 7.5 + - - +
122D LYS 4.3 2.1 - - - +
123D ILE* 3.5 5.7 - - - -
124D LEU* 3.0 24.8 + - - +
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Residues in contact with ASN 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D ASN* 4.7 2.6 - - - +
72D ASP* 3.0 33.7 + - - +
73D ILE 2.8 26.9 + - - +
96D VAL* 4.1 0.7 - - - +
97D ALA* 1.3 86.1 - - - +
99D VAL* 1.3 63.6 + - - +
124D LEU* 3.6 32.0 - - - +
172D GLY 3.6 23.2 - - - +
173D LEU* 3.5 20.8 + - + +
175D GLY* 4.9 4.9 + - - +
177D GLY* 5.4 0.2 - - - -
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Residues in contact with VAL 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D ILE* 3.5 8.5 - - + +
75D ALA* 5.8 0.4 - - + -
83D THR* 4.3 18.2 - - + -
84D LEU* 5.8 0.4 - - + -
87D ILE* 4.2 8.3 - - + -
96D VAL* 3.4 29.2 - - + -
98D ASN* 1.3 72.5 - - - +
100D VAL* 1.3 68.8 + - - +
101D THR* 4.0 20.0 - - + -
123D ILE* 3.7 14.4 - - + -
124D LEU 2.7 10.0 + - - +
125D TYR* 3.3 33.8 - - + -
126D THR* 2.9 24.3 + - - -
172D GLY 5.2 1.0 - - - +
177D GLY* 5.9 0.2 - - - -
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Residues in contact with VAL 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D ILE 2.8 11.3 + - - +
74D VAL* 3.2 10.7 - - + +
75D ALA* 2.8 25.1 + - - +
99D VAL* 1.3 80.0 - - - +
101D THR* 1.3 62.7 + - - +
102D LEU* 3.9 20.9 - - + -
126D THR* 3.2 14.1 - - - +
128D ILE* 4.1 14.6 - - + -
169D ILE* 4.2 16.6 - - + +
172D GLY* 3.8 34.8 - - - +
173D LEU* 4.1 15.0 - - + +
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Residues in contact with THR 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D ALA* 3.2 10.5 - - + -
80D GLY* 4.3 12.1 - - - +
83D THR* 5.7 1.1 - - - -
84D LEU* 5.9 2.2 - - + -
99D VAL* 4.0 19.1 - - + -
100D VAL* 1.3 76.2 - - - +
102D LEU* 1.3 63.1 + - - +
103D GLY 4.0 0.2 - - - -
104D GLY* 4.4 7.4 + - - -
106D ASN* 3.1 39.7 + - - +
125D TYR* 5.6 0.7 - - + -
126D THR 2.9 8.0 + - - +
127D SER* 3.3 16.2 + - - -
128D ILE* 2.8 31.4 + - - +
143D LEU* 5.4 5.8 - - + -
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Residues in contact with LEU 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D PHE* 4.7 0.7 - - + -
22D ILE* 3.7 31.2 - - + -
74D VAL* 4.1 12.6 - - + -
75D ALA 2.7 17.1 + - - +
76D HIS* 3.4 17.4 - - + -
77D SER 3.1 18.0 + - - -
100D VAL* 3.9 19.5 - - + -
101D THR* 1.3 79.9 - - - +
103D GLY* 1.3 66.3 + - - +
128D ILE* 3.5 10.5 - - + -
159D LEU* 3.8 21.1 - - + +
160D LEU* 4.3 14.6 - - + -
165D VAL* 3.9 18.8 - - + -
169D ILE* 4.0 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