Contacts of the strand formed by residues 174 - 180 (chain A) in PDB entry 6PSI
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 LEU 174 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A LEU* 3.2 33.9 - - + +
121A ALA* 3.6 23.1 - - + +
159A ILE 3.5 0.6 - - - +
160A ARG* 3.2 6.4 - - - +
161A VAL* 2.9 41.7 + - + +
164A MET* 3.5 37.5 - - + +
165A GLY* 3.8 10.1 - - - +
172A GLY 2.9 5.2 + - - -
173A ASP* 1.3 73.7 - - - +
175A LEU* 1.3 63.0 + - - +
176A LEU* 3.5 29.8 - - + -
8B LEU* 3.6 12.6 - - + -
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Residues in contact with LEU 175 (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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118A ASP* 6.2 2.7 - - + +
119A LEU 2.9 18.1 + - - +
120A ARG* 3.8 26.9 - - + +
121A ALA 2.8 33.7 + - - +
158A VAL* 3.6 27.1 - - + -
159A ILE 4.0 0.7 - - - -
160A ARG* 3.8 32.3 - - + +
173A ASP 4.6 3.8 - - - +
174A LEU* 1.3 74.4 - - - +
176A LEU* 1.4 53.3 + - - +
177A VAL* 3.0 3.1 + - + -
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Residues in contact with LEU 176 (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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121A ALA 3.7 2.7 - - - -
123A LEU* 4.0 30.5 - - + -
138A VAL* 5.6 2.2 - - + -
145A VAL* 6.3 0.7 - - + -
147A VAL* 3.8 30.1 - - + -
157A SER 2.8 18.4 - - - +
158A VAL* 3.2 1.6 - - - -
159A ILE* 3.0 37.2 + - + +
161A VAL* 3.6 23.3 - - + -
164A MET* 5.7 3.6 - - + -
174A LEU* 3.5 17.5 - - + -
175A LEU* 1.4 67.3 - - - +
177A VAL* 1.3 60.5 + - - +
178A VAL* 3.2 2.0 + - - +
8B LEU* 3.5 33.2 - - + -
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Residues in contact with VAL 177 (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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120A ARG* 3.7 37.7 - - + +
121A ALA 3.0 10.1 + - - +
122A GLU* 3.5 10.7 - - - +
123A LEU 3.1 16.8 + - - +
156A GLY* 4.0 20.6 - - - +
157A SER 3.9 2.9 - - - -
158A VAL* 3.9 20.2 - - + -
175A LEU 3.8 2.5 - - - +
176A LEU* 1.3 66.9 - - - +
178A VAL* 1.3 63.2 + - - +
179A ARG* 3.1 34.5 + - - +
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Residues in contact with VAL 178 (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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123A LEU* 3.5 19.7 - - + +
125A LEU* 3.7 41.1 - - + -
153A VAL* 3.8 11.4 - - + -
154A ARG 3.1 30.3 - - - +
155A GLU* 2.9 21.9 - - - +
156A GLY 3.1 3.8 + - - -
157A SER* 3.1 30.2 + - - +
159A ILE* 5.9 2.0 - - + -
176A LEU 3.2 1.4 + - - +
177A VAL* 1.3 69.2 - - - +
179A ARG* 1.3 60.8 + - - +
180A LEU* 3.8 9.4 + - + -
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Residues in contact with ARG 179 (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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120A ARG* 3.3 17.2 - - - +
122A GLU* 2.9 44.1 + - + -
123A LEU 2.8 12.7 + - - +
124A PRO* 3.0 10.5 - - + +
125A LEU 3.0 20.2 + - - -
155A GLU* 2.9 38.5 + - - +
156A GLY* 5.2 1.0 - - - -
177A VAL* 3.1 25.5 + - - +
178A VAL* 1.3 70.1 - - - +
180A LEU* 1.3 66.3 + - - +
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Residues in contact with LEU 180 (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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125A LEU* 3.4 33.2 - - + +
126A THR 4.8 0.4 - - - +
127A LEU* 3.7 19.3 - - + -
130A ALA* 3.8 22.4 - - + -
153A VAL 3.6 17.5 - - - +
155A GLU* 3.8 13.2 + - - +
178A VAL* 3.8 12.7 + - + -
179A ARG* 1.3 75.0 - - - +
181A LEU* 1.4 67.7 + - - +
182A PRO* 4.5 0.7 - - - +
187A ARG* 4.3 15.3 - - + +
188A LEU* 3.5 46.0 - - + +
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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