Contacts of the strand formed by residues 157 - 162 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B PHE 3.5 0.5 - - - +
134B LEU* 3.3 2.6 - - - -
135B THR* 2.7 52.8 + - - -
137B GLY* 5.3 0.2 - - - -
155B HIS 3.4 10.4 + - - +
156B ARG* 1.3 79.5 - - - +
158B LEU* 1.3 61.5 + - - +
159B MET* 3.8 12.5 + - - +
173B PHE* 3.8 17.0 - - + -
175B SER 3.5 6.3 - - - -
176B VAL* 4.0 10.1 - - + -
177B ALA 3.4 7.1 + - - -
102C LYS* 3.8 30.7 + - + +
104C ASN* 4.2 6.3 + - - +
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Residues in contact with LEU 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B PHE* 4.5 6.3 - - + -
132B PHE* 3.9 27.4 - - + -
133B PHE 3.3 18.6 - - - +
134B LEU* 4.0 10.8 - - + -
157B THR* 1.3 71.4 - - - +
159B MET* 1.3 63.3 + - - +
173B PHE* 4.4 0.7 - - - -
174B GLU* 2.9 45.7 + - + +
175B SER* 2.6 27.5 + - - +
177B ALA* 4.2 4.8 - - + +
180B ALA* 4.0 28.0 - - + -
181B SER 4.6 3.1 - - - +
191B THR* 4.2 20.9 - - + -
192B ILE 4.5 4.9 - - - +
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Residues in contact with MET 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B PHE* 3.9 31.9 - - + -
132B PHE* 3.3 4.3 - - - +
133B PHE* 3.0 50.1 + - + +
135B THR* 4.2 8.7 - - + -
157B THR* 3.8 16.6 + - - +
158B LEU* 1.3 79.2 - - - +
160B SER* 1.3 61.3 + - - +
169B PRO* 5.9 1.6 - - + -
171B SER* 4.0 18.6 - - - +
172B ARG 3.2 10.8 - - - +
173B PHE* 3.7 39.0 - - + +
174B GLU* 3.8 4.9 - - - -
164C GLY 4.3 9.0 - - - +
165C GLU* 4.4 7.6 - - + -
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Residues in contact with SER 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ARG* 2.8 32.3 + - - -
131B THR 3.0 14.1 - - - -
132B PHE* 3.7 17.9 - - - -
133B PHE* 3.8 4.3 - - - -
159B MET* 1.3 76.6 - - - +
161B CYS* 1.3 61.5 + - - +
171B SER* 3.2 3.8 - - - -
172B ARG* 2.7 36.5 + - - +
174B GLU* 2.5 27.4 + - - -
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Residues in contact with CYS 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ARG* 3.5 9.1 - - - +
131B THR* 2.8 35.9 + - - -
133B PHE* 3.8 18.4 - - - -
160B SER* 1.3 76.4 - - - +
162B PRO* 1.3 84.9 - - + +
165B GLU 3.9 18.6 - - - -
167B PRO* 4.2 11.9 - - - -
170B ASN* 3.6 25.6 - - - +
171B SER* 4.0 5.2 - - - +
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Residues in contact with PRO 162 (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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128B GLU* 4.8 7.9 - - - +
129B CYS 4.0 8.7 - - - +
130B ARG* 3.8 16.8 - - - +
131B THR* 4.0 0.5 + - - -
161B CYS* 1.3 94.3 - - + +
163B VAL* 1.3 69.4 + - + +
165B GLU* 2.9 54.2 + - - +
170B ASN 4.4 6.5 - - - +
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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