Contacts of the strand formed by residues 159 - 167 (chain B) in PDB entry 1RHF
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 159 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135B ARG* 3.8 30.6 + - + +
136B GLY* 5.3 1.1 - - - +
155B VAL* 3.8 14.1 - - + +
157B GLN* 2.8 24.8 + - - +
158B SER* 1.3 73.0 + - - +
160B MSE 1.3 66.0 + - - +
161B PHE* 3.5 33.3 - - + -
178B THR* 3.6 1.0 - - - -
179B VAL 2.8 38.7 + - - -
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Residues in contact with MSE 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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135B ARG* 3.5 3.6 - - - -
136B GLY* 2.8 35.7 + - - +
158B SER* 5.9 0.7 - - - +
159B THR* 1.3 77.7 - - - +
161B PHE* 1.3 61.4 + - - +
176B THR* 3.7 31.9 - - + +
177B ALA 3.3 3.4 - - - -
178B THR* 3.7 24.0 - - + +
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Residues in contact with PHE 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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105B PRO* 4.6 0.5 - - - +
116B PHE* 3.9 19.7 - + - -
118B LEU* 3.6 17.7 - - + -
133B TRP* 4.5 6.5 - - + -
134B TRP 3.1 8.3 - - - +
135B ARG* 3.8 32.5 - - + -
140B ILE* 5.8 0.4 - - + -
150B LEU* 3.6 31.0 - - + -
152B VAL* 4.0 13.0 - - + -
155B VAL* 4.4 1.3 - - + -
159B THR* 3.5 34.5 - - + -
160B MSE 1.3 76.9 - - - +
162B SER* 1.3 64.0 + - - +
175B ARG 4.1 0.2 - - - +
176B THR* 3.6 2.7 - - - -
177B ALA* 2.8 37.2 + - + +
179B VAL* 3.7 28.5 - - + -
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Residues in contact with SER 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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105B PRO* 4.6 3.4 - - - -
133B TRP* 3.5 7.0 - - - -
134B TRP* 2.8 47.6 + - - +
161B PHE* 1.3 76.3 - - - +
163B CYS* 1.3 67.0 + - - +
173B SER* 5.9 2.2 - - - -
174B SER* 3.7 14.6 - - - -
175B ARG 3.8 8.5 - - - -
176B THR* 3.9 15.9 + - - +
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Residues in contact with CYS 163 (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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101B PHE* 3.6 16.8 - - + -
105B PRO* 4.7 1.3 - - - -
120B CYS* 2.1 49.6 - - - -
131B ILE* 3.9 6.3 - - + -
132B VAL 3.4 4.0 - - - -
133B TRP* 3.4 31.2 - - - -
134B TRP* 4.8 1.6 - - - -
162B SER* 1.3 77.2 - - - +
164B GLU* 1.3 59.8 + - - +
173B SER* 3.5 5.0 - - - -
174B SER* 2.9 34.6 + - - +
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Residues in contact with GLU 164 (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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168A LEU* 5.5 4.4 - - - +
169A LYS* 5.6 0.3 + - - -
101B PHE* 4.5 0.7 - - - -
130B THR 3.7 0.7 - - - +
131B ILE* 3.4 3.7 - - - -
132B VAL* 2.8 41.1 + - + +
134B TRP* 2.9 42.0 + - + +
162B SER 4.3 0.2 + - - -
163B CYS* 1.3 72.4 - - - +
165B ALA* 1.3 61.1 + - - +
166B HIS* 5.4 0.5 - - - +
171B LEU* 3.3 43.9 - - + +
172B ALA 3.6 9.4 - - - +
173B SER* 4.6 10.3 + - - +
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Residues in contact with ALA 165 (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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99B PRO* 3.8 12.7 - - + +
101B PHE* 3.5 27.5 - - + -
122B ALA* 3.6 22.7 - - + -
129B VAL* 4.0 3.4 - - + -
130B THR 3.3 5.4 - - - -
131B ILE* 4.1 3.4 - - + -
164B GLU* 1.3 72.1 - - - +
166B HIS* 1.3 60.8 + - - +
170B GLY 3.8 0.3 - - - +
171B LEU* 3.2 10.0 - - - +
172B ALA 2.8 31.1 + - - +
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Residues in contact with HIS 166 (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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166A HIS* 3.5 0.7 - + - -
167A ASN 3.4 12.3 - - - -
168A LEU* 2.9 45.0 + - + +
301A ZN 2.1 36.4 - - - -
302A ACT 2.8 12.0 + - + -
99B PRO* 3.8 3.5 - - - +
128B PRO 3.8 0.9 - - - +
129B VAL* 3.4 5.0 - - - +
130B THR* 2.8 50.2 + - + +
164B GLU 5.4 0.4 - - - +
165B ALA* 1.3 76.8 - - - +
167B ASN* 1.3 77.7 + - - +
170B GLY 3.4 5.8 + - - -
171B LEU* 3.8 8.4 - - + +
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Residues in contact with ASN 167 (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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301A ZN 4.6 0.4 - - - -
97B GLY 3.0 25.2 + - - +
98B VAL* 3.6 0.3 - - - -
99B PRO* 3.5 26.6 - - + +
124B GLY* 4.0 5.9 - - - -
125B PRO 3.8 1.4 - - - -
126B PRO* 2.9 37.5 + - - +
128B PRO 3.7 13.9 - - - +
129B VAL* 4.2 1.8 - - + -
166B HIS* 1.3 96.2 + - - +
168B LEU* 1.3 68.3 + - - +
169B LYS 3.2 11.4 + - - -
170B GLY 3.0 20.6 + - - -
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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