Contacts of the strand formed by residues 157 - 162 (chain D) in PDB entry 2HU4
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 157 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102B LYS* 4.0 24.2 - - + +
104B ASN* 3.8 12.7 + - - +
133D PHE 3.5 0.3 - - - +
134D LEU* 3.4 3.0 - - - -
135D THR* 2.7 52.0 + - - -
155D HIS 3.4 13.1 + - - +
156D ARG* 1.3 79.8 - - - +
158D LEU* 1.3 60.4 + - - +
159D MET* 3.7 14.4 + - - +
173D PHE* 3.9 13.4 - - + -
175D SER 3.5 8.3 - - - -
176D VAL* 4.4 7.6 - - + -
177D ALA 3.5 4.9 + - - -
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Residues in contact with LEU 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D PHE* 4.7 5.2 - - + -
132D PHE* 4.1 15.5 - - + -
133D PHE 3.3 30.5 - - - +
134D LEU* 4.0 12.3 - - + -
157D THR* 1.3 70.6 - - - +
159D MET* 1.3 66.1 + - - +
173D PHE* 4.5 0.5 - - - -
174D GLU* 2.9 36.5 + - + +
175D SER* 2.5 34.4 + - - +
177D ALA* 4.1 5.1 - - + +
180D ALA* 3.3 32.1 - - + -
181D SER 4.3 9.4 - - - +
191D THR* 4.7 7.2 - - - -
192D ILE 4.0 8.3 - - - +
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Residues in contact with MET 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B GLY 4.3 10.3 - - - +
165B GLU* 4.7 6.3 - - + -
166B ALA 5.9 0.2 - - - +
115D PHE* 3.9 29.4 - - + -
132D PHE* 3.2 5.9 - - - +
133D PHE* 2.9 47.9 + - + -
135D THR* 4.0 11.0 - - + -
157D THR* 3.7 14.8 + - - +
158D LEU* 1.3 81.4 - - - +
160D SER* 1.3 63.3 + - - +
169D PRO* 5.8 1.6 - - + +
171D SER* 3.9 20.9 - - - +
172D ARG 3.4 10.8 - - - +
173D PHE* 3.8 35.2 - - + +
174D GLU* 3.8 4.5 - - - -
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Residues in contact with SER 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D ARG* 2.9 27.0 + - - -
131D THR 3.1 14.1 - - - -
132D PHE* 3.7 17.3 - - - -
133D PHE* 3.7 5.4 - - - -
159D MET* 1.3 80.3 - - - +
161D CYS* 1.3 62.3 + - - +
171D SER* 3.3 3.5 - - - -
172D ARG* 2.7 35.1 + - - +
174D GLU* 2.6 26.8 + - - -
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Residues in contact with CYS 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D ARG* 3.5 10.2 - - - +
131D THR* 2.7 40.3 + - - +
133D PHE* 3.8 17.7 - - - -
160D SER* 1.3 77.0 - - - +
162D PRO* 1.3 75.4 - - + +
165D GLU 3.6 24.9 - - - -
167D PRO* 3.9 11.9 - - - -
170D ASN* 3.4 23.1 - - - +
171D SER* 4.1 4.7 - - - +
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Residues in contact with PRO 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D GLU* 4.7 9.4 - - - +
129D CYS 3.8 10.1 - - - +
130D ARG* 4.1 15.7 - - + +
131D THR* 4.0 0.9 + - - -
161D CYS* 1.3 95.4 - - + +
163D VAL* 1.3 69.8 + - + +
164D GLY 3.4 0.3 + - - -
165D GLU* 2.7 56.9 + - - +
170D ASN 4.3 6.3 - - - +
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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