Contacts of the strand formed by residues 128 - 134 (chain A) in PDB entry 2QDC
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 TYR 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A LEU* 4.4 2.9 - - + -
95A ILE* 3.7 44.6 - - + -
98A HIS* 3.7 31.6 + - + -
101A LYS* 3.9 32.4 - - + +
102A ASP* 2.4 34.1 + - - -
108A LEU* 4.1 0.3 - - - +
109A PRO* 3.1 42.1 - - + +
114A ARG* 3.9 6.5 - - - +
117A LEU* 3.9 8.7 - - - +
119A ARG* 4.1 5.2 + - - +
126A GLY* 3.7 1.8 - - - -
127A ASP* 1.3 78.2 - - - +
129A ILE* 1.3 65.9 + - - +
130A ASN* 3.6 13.7 + - - -
157A ASP* 4.1 11.6 - - - +
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Residues in contact with ILE 129 (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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101A LYS* 5.8 1.6 - - - -
109A PRO* 3.9 9.7 - - - +
114A ARG* 4.5 1.8 - - - +
115A VAL* 3.4 23.2 + - + +
117A LEU* 3.9 22.4 - - + -
127A ASP 3.7 0.8 + - - -
128A TYR* 1.3 83.7 - - - +
130A ASN* 1.3 64.2 + - - +
131A ALA* 3.0 26.6 + - + +
147A THR* 4.3 5.4 - - - +
148A GLN* 6.3 1.3 - - + +
154A THR* 5.1 6.7 - - + +
157A ASP* 3.9 12.8 - - + +
158A PHE* 3.9 35.7 - - + +
161A MET* 4.0 23.8 - - + -
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Residues in contact with ASN 130 (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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101A LYS 4.3 3.0 + - - +
102A ASP* 3.0 28.1 + - - +
103A ARG 5.2 0.2 - - - +
107A ILE* 2.8 29.0 + - - +
109A PRO* 3.9 10.8 - - - +
128A TYR* 3.6 10.0 + - + -
129A ILE* 1.3 73.7 - - - +
131A ALA* 1.3 51.7 + - - +
147A THR* 2.6 29.7 + - - -
148A GLN* 3.5 33.4 + - - +
272A ALA 5.7 0.2 + - - -
309A ARG* 2.9 41.9 + - - +
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Residues in contact with ALA 131 (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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109A PRO* 3.7 4.9 - - - +
114A ARG* 3.5 5.9 - - - -
115A VAL* 3.1 25.1 + - + -
129A ILE* 3.0 13.4 + - + +
130A ASN* 1.3 76.8 + - - +
132A ASN* 1.3 65.4 + - - +
145A ILE* 3.9 5.6 - - + -
146A ALA 3.2 8.7 - - - +
147A THR* 3.4 18.8 - - - +
161A MET* 3.8 24.2 - - - -
309A ARG* 3.9 1.7 - - - +
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Residues in contact with ASN 132 (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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109A PRO* 3.2 10.6 - - - +
110A ASN 2.9 30.4 + - - +
113A SER* 2.9 24.5 + - - +
114A ARG* 3.4 6.9 - - - +
115A VAL* 3.9 5.8 - - - -
131A ALA* 1.3 73.8 - - - +
133A TYR* 1.3 65.2 + - - +
134A ILE* 3.7 2.9 - - + +
145A ILE* 3.2 2.3 - - - -
146A ALA 2.9 32.3 + - - -
308A ASP 3.4 19.1 + - - +
309A ARG* 2.8 43.2 + - + +
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Residues in contact with TYR 133 (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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113A SER* 2.8 36.6 + - - +
114A ARG 3.7 16.4 - - - -
115A VAL* 3.8 18.1 - - + +
116A CYS 4.7 2.8 + - - -
132A ASN* 1.3 73.5 - - - +
134A ILE* 1.3 65.7 + - - +
142A LYS* 3.6 48.9 + - + +
144A TYR 3.5 3.6 - - - +
145A ILE* 3.9 15.0 - - + -
164A GLN* 4.6 1.4 + - - -
165A GLU* 2.7 44.6 + - - -
265A PRO* 4.6 1.6 - - + -
308A ASP* 3.7 10.2 - - - +
502A GOL 3.4 34.9 + - - +
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Residues in contact with ILE 134 (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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132A ASN* 3.7 12.1 - - + +
133A TYR* 1.3 83.4 - - - +
135A ARG* 1.3 75.8 + - - +
142A LYS 4.4 2.9 - - - -
143A VAL 3.1 22.9 + - - -
144A TYR* 2.8 24.5 + - + +
146A ALA* 3.7 25.1 - - + +
281A ILE* 4.2 16.6 - - + -
305A LEU* 3.5 26.5 - - + +
308A ASP* 3.5 19.3 - - + +
309A ARG* 3.8 22.7 - - + -
312A MET* 4.1 6.7 - - + -
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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