Contacts of the strand formed by residues 138 - 146 (chain A) in PDB entry 1NHX
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 THR 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A VAL* 4.9 4.3 - - + +
40A PRO* 4.5 0.7 - - - -
42A HIS* 3.3 32.6 + - + +
44A HIS* 3.8 25.4 - - + +
137A ARG* 1.3 76.1 - - - +
139A MET* 1.3 62.1 + - - +
140A TYR* 3.6 36.1 + - + +
162A ASP* 3.4 23.9 - - - +
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Residues in contact with MET 139 (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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31A LEU* 3.6 29.6 - - + -
34A ASN* 3.7 35.7 - - + +
35A ALA* 4.0 5.8 - - - +
38A CYS* 4.2 4.5 - - + -
40A PRO* 3.7 19.6 - - + +
42A HIS 2.7 10.1 + - - +
43A ILE* 3.4 12.7 - - + +
44A HIS 2.9 25.7 + - - +
134A MET* 3.7 33.2 - - + -
138A THR* 1.3 69.9 - - - +
140A TYR* 1.3 71.0 + - - +
160A LEU* 4.1 19.5 - - + -
161A THR 3.5 4.9 - - - +
193A LEU* 4.9 0.4 - - + -
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Residues in contact with TYR 140 (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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44A HIS* 3.3 39.3 - + + +
46A CYS* 4.1 4.7 - - - -
56A LEU* 3.8 33.0 - - + +
59A GLN* 4.3 8.5 + - - -
138A THR* 3.6 32.9 + - + +
139A MET* 1.3 74.6 - - - +
141A VAL* 1.3 61.2 + - - +
142A ILE* 3.9 0.7 - - + -
159A GLU 3.4 1.6 - - - +
160A LEU* 3.2 7.4 - - - -
161A THR* 2.6 41.8 + - + +
162A ASP 4.6 1.3 - - - -
163A SER 4.3 6.3 - - - -
164A PRO* 4.1 29.6 - - + +
167A VAL* 3.5 32.8 - - + -
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Residues in contact with VAL 141 (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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23A LEU* 5.3 1.8 - - + -
27A VAL* 4.9 11.2 - - + -
31A LEU* 3.7 37.7 - - + -
43A ILE* 3.9 17.7 - - + -
44A HIS 2.8 13.0 + - - +
45A ILE* 4.0 17.2 - - + +
46A CYS* 2.9 24.4 + - - +
139A MET* 4.4 1.6 - - + +
140A TYR* 1.3 74.7 - - - +
142A ILE* 1.3 61.0 - - - +
143A PRO* 3.2 10.5 - - + +
158A ILE* 3.9 17.0 - - + -
159A GLU 3.8 1.8 - - - -
160A LEU* 3.7 17.3 - - + -
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Residues in contact with ILE 142 (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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46A CYS* 4.1 6.5 - - - -
140A TYR 4.6 0.9 - - - +
141A VAL* 1.3 71.9 - - - +
143A PRO* 1.3 61.6 - - - +
144A PHE* 3.5 14.1 + - + -
158A ILE* 3.4 6.2 - - - -
159A GLU* 2.8 47.2 + - + +
161A THR* 3.7 27.1 - - + -
166A VAL* 4.0 11.4 - - + -
167A VAL* 3.7 32.3 - - + -
170A MET* 4.0 17.9 - - + -
176A MET* 3.2 31.9 - - + -
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Residues in contact with PRO 143 (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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45A ILE* 5.3 0.9 - - + -
46A CYS* 3.7 22.7 - - + +
141A VAL* 3.2 15.3 - - + +
142A ILE* 1.3 82.9 - - + +
144A PHE* 1.3 58.4 + - - +
157A GLY 3.8 5.8 - - - +
158A ILE* 3.8 14.8 - - + -
176A MET* 3.3 3.5 - - - +
177A GLY* 2.8 45.3 + - - +
180A VAL* 3.7 11.3 - - + +
181A LEU* 3.7 37.0 - - + -
184A LEU* 6.3 0.2 - - + -
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Residues in contact with PHE 144 (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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142A ILE* 3.5 15.3 - - + -
143A PRO* 1.3 75.0 - - - +
145A SER* 1.3 60.4 + - - +
146A MET* 3.7 23.8 - - + -
156A ILE* 3.4 5.0 - - - +
157A GLY* 2.9 60.0 + - - +
158A ILE 3.9 1.3 - - - -
159A GLU* 3.7 17.9 - - + -
170A MET* 3.5 20.6 - - + -
174A THR* 3.4 24.7 - - + +
175A ARG 3.1 5.2 - - - +
176A MET* 4.5 0.2 - - - -
180A VAL* 3.6 6.2 - - - +
192A CYS* 4.0 11.0 - - - -
242A GLY* 3.7 28.0 - - - -
246A PHE* 3.8 20.6 - + - -
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Residues in contact with SER 145 (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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144A PHE* 1.3 72.8 - - - +
146A MET* 1.3 66.4 + - - +
147A GLY 3.0 23.8 + - - +
148A PRO 4.2 2.4 + - - -
149A LEU* 4.2 12.3 - - - +
150A GLY 4.8 0.5 + - - -
154A SER* 4.0 11.6 - - - -
155A LYS 3.6 5.3 + - - -
156A ILE* 4.1 15.2 - - - +
174A THR* 3.9 6.1 - - - -
175A ARG* 2.8 39.5 + - - +
180A VAL* 3.9 10.9 - - - +
328A PRO 4.3 0.7 - - - +
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Residues in contact with MET 146 (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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144A PHE* 3.7 13.7 - - + -
145A SER* 1.3 70.8 - - - +
147A GLY* 1.3 58.5 + - - +
154A SER* 3.3 5.9 - - - -
155A LYS 2.7 32.1 + - - +
173A MET 4.9 0.2 - - - +
174A THR* 3.7 30.3 - - + -
242A GLY* 3.2 26.0 - - - +
243A LYS* 4.3 1.3 - - - +
246A PHE* 3.8 29.6 - - + -
247A ALA* 4.0 10.8 - - + -
314A TRP* 3.5 24.9 - - + -
328A PRO* 3.3 26.9 - - + +
329A GLU* 4.4 12.3 - - + +
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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