Contacts of the strand formed by residues 157 - 168 (chain A) in PDB entry 1NH1
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 LEU 157 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A ILE* 3.3 4.9 - - - -
149A MET* 2.8 59.2 + - + +
151A ASP* 4.5 5.4 - - + -
154A PHE* 3.7 16.4 - - + -
155A GLY 3.5 10.8 - - - +
156A ASP* 1.3 76.7 - - - +
158A ASN* 1.3 68.4 + - - +
159A VAL* 3.4 3.7 + - + -
181A ALA* 4.7 2.7 - - + -
183A ASP* 4.1 8.7 - - + +
186A TYR* 3.9 24.7 - - + -
187A LEU* 3.6 26.0 - - + -
212A PRO* 3.7 32.8 - - + -
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Residues in contact with ASN 158 (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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146A ASP* 6.6 0.7 - - + -
147A GLU 3.6 6.1 - - - +
148A ILE* 2.9 27.4 - - + +
157A LEU* 1.3 72.8 - - - +
159A VAL* 1.3 52.0 + - - +
181A ALA* 3.4 4.3 - - - +
182A THR* 2.6 55.3 + - + +
183A ASP* 2.5 36.4 + - - +
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Residues in contact with VAL 159 (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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145A HIS 3.6 0.3 - - - +
146A ASP* 3.6 2.5 - - - -
147A GLU* 2.8 51.9 + - + +
148A ILE 4.6 0.2 - - - -
149A MET* 3.3 50.5 - - + -
157A LEU* 3.9 3.1 - - + +
158A ASN* 1.3 79.9 - - - +
160A LYS* 1.3 62.7 + - - +
161A VAL* 3.4 20.9 - - + -
179A ARG* 4.2 7.9 - - + +
180A VAL 3.4 9.9 - - - +
181A ALA* 3.8 12.8 - - - +
182A THR* 5.0 1.8 - - - -
212A PRO 4.7 1.3 - - - +
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Residues in contact with LYS 160 (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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138A VAL* 3.8 11.6 - - + +
139A VAL* 3.9 54.9 + - + +
144A ALA* 4.6 12.6 + - + +
145A HIS 3.7 6.1 - - - -
146A ASP* 2.8 38.4 + - - +
159A VAL* 1.3 71.4 - - - +
161A VAL* 1.3 61.8 + - - +
179A ARG* 3.7 1.4 - - - -
180A VAL 2.9 35.3 + - - +
182A THR* 4.8 13.4 - - + +
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Residues in contact with VAL 161 (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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143A ASP 4.1 0.2 - - - +
144A ALA* 3.3 4.4 - - - +
145A HIS* 2.7 70.9 + - + +
147A GLU* 3.6 15.7 - - + +
159A VAL* 3.4 29.2 - - + +
160A LYS* 1.3 80.6 - - - +
162A TYR* 1.3 61.2 + - - +
163A ARG* 3.8 17.3 - - + +
177A THR* 4.1 7.9 - - + -
178A PHE 3.4 9.9 - - - +
179A ARG* 3.5 15.3 - - - -
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Residues in contact with TYR 162 (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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138A VAL* 4.4 6.5 - - + +
141A HIS* 3.6 33.1 + + + -
143A ASP* 3.7 27.1 + - + -
144A ALA* 4.3 6.7 - - + +
161A VAL* 1.3 74.4 - - - +
163A ARG* 1.3 68.1 + - - +
164A GLN* 3.7 17.2 + - + +
165A THR 5.5 0.2 + - - -
177A THR* 3.5 1.7 - - - -
178A PHE* 2.8 60.3 + + + +
301A MET 3.4 9.9 - - - -
302A LEU* 3.1 37.0 + - + -
303A SER* 3.3 19.9 + - - -
304A GLY* 3.7 3.3 + - - -
307A GLU* 4.3 3.6 + - - -
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Residues in contact with ARG 163 (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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143A ASP 5.2 0.8 + - - -
145A HIS* 3.6 15.6 + - + -
147A GLU* 3.1 38.1 + - - -
161A VAL* 3.8 12.2 + - + -
162A TYR* 1.3 82.6 - - - +
164A GLN* 1.3 63.4 + - - +
165A THR* 3.6 16.7 + - + +
174A PRO* 6.2 3.2 - - + +
176A ASN 4.0 2.9 - - - -
177A THR* 3.3 30.2 + - + +
179A ARG* 3.8 16.4 - - - +
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Residues in contact with GLN 164 (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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162A TYR* 3.7 14.3 + - + +
163A ARG* 1.3 72.9 - - - +
165A THR* 1.3 62.9 + - - +
174A PRO* 3.5 2.6 - - - +
175A LEU* 2.7 54.9 + - - +
176A ASN* 2.8 42.1 + - - +
177A THR* 5.3 0.5 + - - -
256A TRP* 3.3 6.9 + - + -
260A SER* 3.1 16.7 + - - -
300A ALA 2.8 24.4 - - - +
301A MET 3.1 21.5 + - - +
303A SER 3.0 17.5 - - - +
304A GLY* 5.4 0.4 - - - -
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Residues in contact with THR 165 (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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163A ARG* 3.6 18.3 + - + +
164A GLN* 1.3 82.2 - - - +
166A ALA* 1.3 64.0 + - - +
172A VAL* 3.9 18.9 - - + +
173A ILE 3.0 13.9 - - - +
174A PRO* 4.4 7.2 - - + -
175A LEU* 4.2 2.5 - - - +
256A TRP* 3.8 13.8 - - - -
304A GLY* 5.0 5.5 - - - -
305A GLU 5.2 0.7 + - - -
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Residues in contact with ALA 166 (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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165A THR* 1.3 73.5 - - - +
167A TYR* 1.3 61.6 + - - +
168A LEU 3.8 0.2 + - - -
171A ASN 3.4 1.9 - - - +
172A VAL* 3.1 8.5 - - - -
173A ILE* 2.7 39.2 + - + +
175A LEU* 3.7 12.3 - - + -
256A TRP* 3.2 29.2 - - + -
257A TRP* 3.3 24.2 - - + -
305A GLU* 6.0 0.4 - - - -
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Residues in contact with TYR 167 (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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166A ALA* 1.3 73.6 - - - +
168A LEU* 1.3 60.3 + - - +
169A HIS* 4.0 7.6 - - - -
170A GLY* 3.2 41.0 + - - -
171A ASN 3.8 1.6 - - - -
172A VAL* 4.1 18.8 - - + +
229A HIS* 5.4 1.6 + - - -
257A TRP* 3.4 18.5 - - - -
305A GLU* 4.5 9.5 + - - +
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Residues in contact with LEU 168 (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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167A TYR* 1.3 74.1 - - - +
169A HIS* 1.3 104.0 + - + +
170A GLY 3.1 0.2 - - - -
171A ASN* 2.9 37.9 + - + +
173A ILE* 4.8 11.4 - - + -
225A ILE* 3.8 50.9 - - + +
226A ILE* 4.6 0.9 - - - +
229A HIS* 3.8 25.4 - - + +
257A TRP* 3.9 22.0 - - + -
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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