Contacts of the strand formed by residues 170 - 176 (chain Q) in PDB entry 2IAN
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 VAL 170 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132Q PHE 3.9 0.5 - - - +
133Q ARG* 3.8 1.0 - - - +
134Q ASN* 2.9 40.6 + - - +
135Q GLY 4.8 0.2 + - - -
168Q GLY 3.4 13.4 + - - +
169Q GLU* 1.3 71.8 - - - +
171Q TYR* 1.3 62.8 + - - +
172Q THR* 4.0 8.6 + - - +
187Q GLU* 3.5 38.8 - - + +
188Q TRP 3.9 3.6 - - - +
189Q ARG* 4.2 17.0 - - + -
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Residues in contact with TYR 171 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115Q LEU* 3.7 17.5 - - + -
131Q TRP* 4.1 7.2 - - + -
132Q PHE 3.2 6.1 - - - -
133Q ARG* 3.0 59.6 + - + -
161Q LEU* 3.7 18.2 - - + -
163Q THR* 3.5 31.4 + - + -
165Q PRO* 3.6 22.0 - - + +
169Q GLU* 3.4 30.4 + - + -
170Q VAL* 1.3 75.0 - - - +
172Q THR* 1.3 62.4 + - - +
173Q CYS 4.3 0.2 + - - -
186Q VAL 4.1 0.3 - - - +
187Q GLU* 3.1 4.7 - - - +
188Q TRP* 2.8 52.6 + + + +
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Residues in contact with THR 172 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130Q ARG 3.5 4.7 - - - +
131Q TRP* 3.6 5.6 - - - -
132Q PHE* 2.6 52.0 + - + +
135Q GLY* 5.4 3.7 + - - -
170Q VAL* 4.0 10.0 + - - +
171Q TYR* 1.3 75.3 + - - +
173Q CYS* 1.3 65.2 + - - +
174Q GLN* 3.5 3.9 + - + +
185Q THR* 4.2 30.5 - - + -
186Q VAL 3.7 4.9 - - - +
187Q GLU* 3.8 16.4 + - + +
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Residues in contact with CYS 173 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99Q VAL* 4.5 3.5 - - + +
101Q VAL* 3.7 18.4 - - + -
117Q CYS* 2.0 51.6 - - + -
129Q VAL* 3.3 21.5 - - - -
130Q ARG 3.9 3.1 - - - -
131Q TRP* 3.8 13.3 - - + -
172Q THR* 1.3 73.0 - - - +
174Q GLN* 1.3 57.0 + - - +
175Q VAL* 4.0 6.3 + - - +
184Q LEU 3.6 1.9 - - - +
185Q THR* 3.5 4.7 - - - -
186Q VAL* 2.9 30.7 + - - +
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Residues in contact with GLN 174 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128Q GLU 3.4 4.9 - - - +
129Q VAL* 3.4 1.9 - - - +
130Q ARG* 2.9 47.7 + - + +
132Q PHE* 3.8 32.8 - - + -
172Q THR* 3.5 2.2 + - + +
173Q CYS* 1.3 72.9 - - - +
175Q VAL* 1.3 63.4 + - - +
176Q GLU* 3.2 33.8 - - - +
183Q PRO* 4.1 17.1 - - + +
184Q LEU 3.7 1.8 - - - -
185Q THR* 3.7 22.2 - - + +
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Residues in contact with VAL 175 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97Q PRO* 4.4 16.8 - - + -
99Q VAL* 3.8 25.6 - - + -
119Q VAL* 4.0 9.2 - - + -
127Q ILE* 3.8 33.0 - - + -
128Q GLU 3.4 2.7 - - - +
129Q VAL* 4.0 19.5 - - + -
173Q CYS* 4.1 7.9 - - - -
174Q GLN* 1.3 79.1 - - - +
176Q GLU* 1.3 66.8 + - - +
177Q HIS* 4.5 1.8 - - + -
180Q VAL* 4.8 3.8 - - - +
183Q PRO* 3.3 4.8 - - - +
184Q LEU* 2.9 43.2 + - + +
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Residues in contact with GLU 176 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127Q ILE* 3.5 4.3 - - - +
128Q GLU* 3.0 52.8 + - - +
130Q ARG* 3.2 30.6 + - - -
174Q GLN* 3.2 19.0 - - - +
175Q VAL* 1.3 72.3 - - - +
177Q HIS* 1.3 64.3 + - - +
180Q VAL* 5.6 0.7 - - - -
183Q PRO* 3.9 22.3 - - + +
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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