Contacts of the strand formed by residues 173 - 181 (chain A) in PDB entry 4OD2
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 TYR 173 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A GLU* 4.3 14.9 + - - -
103A LYS* 5.8 1.7 + - - -
105A THR* 5.5 2.5 - - + +
139A ASP 2.9 25.3 + - - -
140A PHE* 2.7 46.4 + - + +
141A TYR* 4.0 20.4 - + - -
142A PRO 4.2 0.2 - - - -
143A GLY* 3.2 36.1 - - - -
165A PRO* 3.9 7.9 - - + -
166A SER* 3.3 28.3 - - - -
167A LYS* 3.7 35.2 + - + +
168A GLN* 3.4 1.0 - - - +
171A ASN 4.1 7.2 - - - -
172A LYS* 1.3 76.8 - - - +
174A ALA* 1.3 61.4 + - - +
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Residues in contact with ALA 174 (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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137A ILE 3.3 14.1 - - - +
138A SER* 3.9 1.8 - - - -
140A PHE* 3.5 4.9 - - - -
164A THR 4.8 0.2 - - - +
165A PRO* 3.3 5.0 - - - +
166A SER* 3.1 30.3 + - - +
168A GLN* 3.7 26.2 - - + +
173A TYR* 1.3 78.4 - - - +
175A ALA* 1.3 61.4 + - - +
172B HIS* 4.6 4.7 - - - +
174B PHE* 4.4 12.8 - - + -
175B PRO* 5.7 2.8 - - - +
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Residues in contact with ALA 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LEU* 4.0 0.2 - - - -
137A ILE* 2.8 48.6 + - + +
140A PHE* 3.8 13.4 - - + -
145A VAL* 4.7 4.9 - - + -
147A VAL* 5.6 0.7 - - + -
162A THR* 5.4 3.4 - - + -
163A THR* 3.7 21.5 - - - +
165A PRO* 4.2 11.4 - - + -
174A ALA* 1.3 76.8 - - - +
176A SER* 1.3 62.8 + - - +
174B PHE* 4.3 5.2 - - - -
175B PRO* 6.2 1.8 - - - -
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Residues in contact with SER 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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135A CYS 3.7 4.5 - - - -
136A LEU* 3.8 23.3 - - - -
137A ILE* 5.5 0.7 - - - -
162A THR* 3.4 5.5 - - - +
163A THR* 2.8 55.6 + - - +
175A ALA* 1.3 75.0 - - - +
177A SER* 1.3 60.9 + - - +
178A TYR* 3.8 20.3 + - - -
174B PHE* 4.1 11.7 - - - +
175B PRO* 3.8 10.9 + - - +
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Residues in contact with SER 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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134A VAL* 3.8 0.7 - - - +
135A CYS* 2.9 39.6 + - - -
136A LEU* 5.4 0.2 - - - +
137A ILE* 5.2 1.1 - - - -
147A VAL* 3.6 24.6 - - - +
149A TRP* 2.9 32.4 + - - -
160A VAL* 4.1 0.2 - - - +
161A GLU 3.3 4.1 + - - -
162A THR* 3.1 21.3 + - - -
176A SER* 1.3 76.4 - - - +
178A TYR* 1.3 65.2 + - - +
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Residues in contact with TYR 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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132A THR* 4.4 11.0 - - + -
133A LEU 3.4 5.6 - - - +
134A VAL* 3.8 34.1 - - + -
136A LEU* 4.6 0.2 - - - +
149A TRP* 4.2 3.6 - - - -
159A GLY 3.3 1.6 - - - +
160A VAL* 3.2 7.6 - - - +
161A GLU* 2.8 42.8 + - + +
176A SER* 3.8 34.5 + - - -
177A SER* 1.3 76.7 + - - +
179A LEU* 1.3 60.0 + - - +
180A SER* 4.0 2.7 - - - +
149B LEU* 3.9 15.5 - - + -
151B LYS* 5.9 1.1 - - - +
174B PHE* 4.8 1.4 - - - +
175B PRO 4.9 1.3 + - - -
177B VAL* 3.7 30.5 - - + -
179B GLN* 6.0 2.2 - - - +
185B SER* 4.4 11.7 - - - -
186B LEU* 3.6 5.2 - - - -
187B SER* 3.3 35.0 + - - -
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Residues in contact with LEU 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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131A ALA 3.5 1.6 - - - +
132A THR* 3.4 5.5 - - - -
133A LEU* 3.0 40.2 + - + +
149A TRP* 3.5 42.8 - - + -
156A VAL* 3.9 20.4 - - + -
158A ALA 3.9 7.4 - - - +
159A GLY 4.1 2.7 - - - -
160A VAL* 3.7 25.6 - - + -
178A TYR* 1.3 72.3 - - - +
180A SER* 1.3 59.6 + - - +
181A LEU* 3.8 30.5 - - + -
192A TYR* 3.8 20.0 - - + -
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Residues in contact with SER 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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131A ALA 3.6 4.5 - - - -
132A THR* 3.6 2.1 + - - +
159A GLY* 2.9 30.1 + - - -
178A TYR* 4.0 2.8 - - - +
179A LEU* 1.3 72.9 - - - +
181A LEU* 1.3 69.8 + - - +
151B LYS* 2.8 30.5 + - - -
179B GLN* 4.5 5.0 + - - -
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Residues in contact with LEU 181 (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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130A LYS* 4.0 1.4 - - - -
131A ALA* 2.8 38.0 + - + +
133A LEU* 3.8 22.9 - - + -
156A VAL* 4.8 5.8 - - + -
158A ALA 4.8 5.6 - - - +
179A LEU* 3.8 24.5 - - + +
180A SER* 1.3 82.8 - - - +
182A THR* 1.3 68.5 + - - +
185A GLN* 3.7 25.6 - - + +
186A TRP* 4.8 9.0 - - + +
192A TYR* 3.7 40.4 - - + +
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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