Contacts of the strand formed by residues 157 - 161 (chain B) in PDB entry 1N99
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 GLN 157 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A GLY* 3.2 26.3 + - - +
233A LEU* 3.5 18.7 - - - +
135B GLY* 4.5 7.3 - - - -
136B ILE 3.4 12.6 - - - +
137B PHE* 3.5 24.6 - - + -
155B GLY 3.5 0.6 + - - -
156B ASP* 1.3 73.3 - - - +
158B VAL* 1.3 65.8 + - - +
159B LEU* 3.6 22.0 + - + +
190B ILE* 3.3 6.8 - - - +
191B ARG* 2.8 66.3 + - + +
194B PRO* 3.8 12.0 - - + +
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Residues in contact with VAL 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B LEU* 4.0 27.4 - - + -
136B ILE* 2.9 30.5 + - + +
138B VAL* 4.1 12.6 - - + +
156B ASP 4.7 0.4 - - - +
157B GLN* 1.3 76.1 + - - +
159B LEU* 1.3 61.5 + - - +
160B GLN 3.6 21.5 - - - +
161B ILE* 3.7 22.4 - - + -
166B CYS* 3.4 20.2 - - - +
188B MSE 4.4 9.2 - - + -
189B THR 3.6 5.6 - - - +
190B ILE* 4.0 17.0 - - + -
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Residues in contact with LEU 159 (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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228A ALA 4.9 2.3 - - - +
229A ARG 4.2 12.8 - - - +
230A ASN* 4.3 3.6 - - - +
231A GLY* 3.8 13.9 - - - +
112B PRO* 4.0 29.4 - - + -
157B GLN* 3.6 37.2 - - + +
158B VAL* 1.3 74.5 - - - +
160B GLN* 1.3 81.4 + - - +
165B ASN* 3.5 1.0 - - - +
166B CYS* 3.0 23.6 + - - +
167B ALA 4.6 0.9 + - - -
189B THR* 2.8 18.3 + - + +
191B ARG* 3.9 35.7 - - + +
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Residues in contact with GLN 160 (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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229A ARG* 2.8 32.5 + - - +
158B VAL* 3.6 3.5 - - - +
159B LEU* 1.3 94.0 + - - +
161B ILE* 1.3 65.6 + - - +
162B ASN 4.2 0.4 - - - -
163B GLY* 4.2 15.0 - - - +
164B GLU 3.1 20.9 - - - +
165B ASN* 2.9 24.7 + - - +
166B CYS* 4.0 1.6 - - - -
188B MSE 3.3 4.0 - - - -
189B THR* 2.9 58.6 + - - +
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Residues in contact with ILE 161 (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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129B LEU* 4.0 18.6 - - + -
158B VAL* 3.7 13.7 - - + -
160B GLN* 1.3 77.3 - - - +
162B ASN* 1.3 86.4 + - - +
163B GLY 3.0 0.9 - - - -
164B GLU* 3.0 24.4 + - - +
166B CYS* 3.8 9.0 - - - -
169B TRP* 3.9 29.1 - - + -
174B ALA 5.3 0.2 - - - +
177B VAL* 4.4 13.6 - - + +
178B LEU* 3.9 26.2 - - + -
181B ALA* 5.8 1.3 - - + -
186B ILE* 4.1 13.2 - - + -
187B THR 3.4 8.7 - - - +
188B MSE 4.2 7.6 - - + -
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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