Contacts of the strand formed by residues 166 - 171 (chain B) in PDB entry 1NDD
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 166 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B LYS* 3.5 24.0 - - + +
106B LYS* 4.0 20.0 - - + +
112B GLU* 3.8 17.3 - - - +
144B ILE 4.6 0.3 - - - +
145B TYR* 3.3 19.8 - - - -
146B SER 5.3 0.2 + - - -
164B GLY 3.9 9.6 - - - +
165B SER* 1.3 77.0 - - - +
167B LEU* 1.3 74.0 + - - +
168B HIS* 4.1 17.6 + - + -
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Residues in contact with LEU 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B ILE* 3.8 26.2 - - + -
104B LYS 2.8 14.2 + - - +
105B VAL* 3.4 9.9 - - + -
106B LYS* 2.8 29.1 + - - +
126B ILE* 4.0 20.4 - - + -
143B LEU* 4.3 13.2 - - + -
144B ILE 3.5 6.5 - - - +
145B TYR* 3.4 31.6 - - + -
150B MET* 4.1 17.5 - - + -
161B ILE* 3.7 26.2 - - + -
165B SER* 4.9 2.5 - - - +
166B VAL* 1.3 75.7 - - - +
168B HIS* 1.3 63.2 + - - +
169B LEU 4.1 0.2 - - - -
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Residues in contact with HIS 168 (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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106B LYS* 3.4 36.8 + - + +
107B THR 5.9 2.0 - - - -
108B LEU* 6.4 2.2 - - + -
142B ARG 3.5 1.6 - - - +
143B LEU* 3.4 5.7 - - - -
144B ILE* 2.8 53.8 + - + +
145B TYR* 5.8 0.8 - - - -
146B SER 6.1 0.6 + - - -
166B VAL* 4.1 25.8 + - + -
167B LEU* 1.3 74.8 - - - +
169B LEU* 1.3 62.5 + - - +
170B VAL* 5.3 4.0 - - + -
347D GLY 5.7 1.8 - - - +
349D GLN* 4.5 27.5 + - + +
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Residues in contact with LEU 169 (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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105B VAL* 3.6 24.0 - - + -
106B LYS 2.8 17.4 + - - +
107B THR* 3.9 21.5 - - + +
108B LEU 4.4 2.3 + - - -
113B ILE* 6.0 0.4 - - + -
130B VAL* 4.0 22.0 - - + -
134B GLU* 6.1 0.2 - - + -
136B ILE* 5.4 2.7 - - + -
141B GLN* 3.7 38.1 - - + +
142B ARG 3.5 7.4 - - - +
143B LEU* 4.0 8.1 - - + -
167B LEU 4.1 0.6 + - - -
168B HIS* 1.3 72.4 - - - +
170B VAL* 1.3 79.2 + - - +
171B LEU* 6.1 0.4 - - + -
271C LEU* 3.6 29.0 - - + +
273C LEU* 5.0 6.5 - - + -
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Residues in contact with VAL 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B LEU* 3.9 23.3 - - + -
142B ARG* 2.9 48.7 + - + +
144B ILE* 4.1 5.6 - - + -
168B HIS* 5.3 3.4 - - + -
169B LEU* 1.3 87.6 - - - +
171B LEU* 1.3 62.6 + - - +
2001B CL 3.9 8.1 - - + -
208C LEU* 6.0 5.6 - - + -
209C THR* 3.6 26.0 - - + -
347D GLY* 3.5 27.4 - - - +
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Residues in contact with LEU 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ILE* 3.8 24.2 - - + -
140B GLN* 3.3 15.0 - - + +
141B GLN* 5.5 0.4 - - - -
169B LEU* 6.1 0.4 - - + -
170B VAL* 1.3 74.5 - - - +
172B ALA* 1.3 53.2 + - - +
173B LEU* 4.1 1.8 - - + -
2001B CL 3.4 10.7 - - + +
207C THR* 3.5 20.5 + - + -
208C LEU 5.0 0.2 + - - -
209C THR* 2.7 28.9 + - - +
236C ILE* 3.9 19.3 - - + -
269C LEU* 3.8 37.7 - - + +
270C VAL 4.3 1.1 - - - -
271C LEU* 3.7 42.6 - - + +
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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