Contacts of the strand formed by residues 174 - 183 (chain A) in PDB entry 3F12
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 174 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A THR* 4.2 15.8 - - - +
106A GLU* 5.7 0.2 + - - -
139A ASN* 3.1 8.6 - - - -
140A PHE* 3.0 45.3 + - + +
141A TYR* 4.1 9.2 - + - -
143A ARG* 3.8 52.0 - - + +
164A VAL* 4.1 13.5 - - + -
165A THR* 3.4 23.8 - - - -
166A GLU* 3.9 1.8 - - - -
167A GLN* 3.3 55.1 + - + +
173A THR* 1.3 79.3 - - - +
175A SER* 1.3 61.7 + - - +
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Residues in contact with SER 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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137A LEU 3.3 9.2 - - - -
138A ASN* 3.3 10.2 + - - -
139A ASN* 3.3 1.7 + - - -
140A PHE* 3.6 2.0 - - - -
164A VAL* 2.9 29.1 - - - +
165A THR* 2.9 21.7 + - - -
174A TYR* 1.3 76.7 + - - +
176A LEU* 1.3 62.3 + - - +
176B HIS* 3.0 30.7 + - - -
178B PHE* 3.3 20.0 - - - -
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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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135A CYS 3.5 1.0 - - - +
136A LEU* 3.5 8.3 - - - +
137A LEU* 3.0 49.2 + - + -
140A PHE* 4.1 13.5 - - + -
143A ARG 5.8 0.4 - - - +
145A ALA 3.8 19.3 - - - +
147A VAL* 3.9 23.8 - - + -
162A GLU* 3.8 28.3 - - + +
163A SER 3.1 12.3 - - - +
164A VAL* 4.0 15.7 - - + -
175A SER* 1.3 79.4 - - - +
177A SER* 1.3 61.7 + - - +
178A SER* 3.8 14.4 - - - +
178B PHE* 3.2 5.7 - - - -
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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* 3.9 6.7 - - - +
135A CYS 3.6 4.7 - - - -
136A LEU* 5.1 1.1 - - - +
161A GLN 3.1 13.9 - - - +
162A GLU* 3.1 12.1 - - - -
163A SER* 3.0 16.4 + - - -
176A LEU* 1.3 71.6 - - - +
178A SER* 1.3 58.7 + - - +
179A THR* 3.6 12.3 + - - -
178B PHE* 3.3 37.1 - - - -
191B SER* 3.4 21.2 + - - -
193B VAL* 6.0 0.4 - - - -
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Residues in contact with SER 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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134A VAL* 3.6 0.4 - - - -
135A CYS* 2.7 43.0 + - - -
147A VAL* 4.0 27.4 - - - +
149A TRP* 2.9 32.6 + - - -
160A SER* 4.0 6.9 - - - -
161A GLN 3.5 4.0 + - - -
162A GLU* 3.7 16.9 + - - +
176A LEU* 3.8 7.4 - - - +
177A SER* 1.3 71.1 - - - +
179A THR* 1.3 59.0 + - - +
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Residues in contact with THR 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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132A SER* 3.4 26.2 - - - +
133A VAL 3.4 13.5 - - - +
134A VAL* 3.9 16.9 - - + +
149A TRP* 4.2 0.7 - - - -
159A ASN 4.0 0.2 - - - +
160A SER* 3.0 5.3 - - - -
161A GLN* 3.0 39.4 + - - +
177A SER* 3.6 15.1 + - - -
178A SER* 1.3 74.7 + - - +
180A LEU* 1.3 59.7 + - - +
181A THR* 3.9 6.8 + - - +
153B LEU* 5.0 8.6 - - + +
181B VAL* 6.0 1.9 - - - +
189B SER* 5.6 5.3 + - - +
191B SER* 5.1 2.8 + - - -
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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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131A ALA 4.0 0.3 - - - +
132A SER* 3.4 3.1 + - - -
133A VAL* 2.8 56.7 + - + +
149A TRP* 3.6 49.7 - - + +
150A LYS 5.9 0.2 - - - +
151A VAL* 4.3 14.1 - - + -
156A GLN* 4.3 3.1 - - - +
159A ASN* 3.5 43.7 - - - +
160A SER* 4.1 2.2 - - - +
179A THR* 1.3 71.6 - - - +
181A THR* 1.3 60.7 + - - +
182A LEU* 3.9 21.5 - - + -
193A TYR* 4.4 4.5 - - + -
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Residues in contact with THR 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 THR* 4.2 13.9 - - + +
131A ALA 3.7 5.2 - - - +
132A SER* 3.0 17.9 + - - +
159A ASN* 3.1 25.4 + - - +
179A THR* 3.9 7.1 + - - +
180A LEU* 1.3 73.7 - - - +
182A LEU* 1.3 78.0 + - - +
155B LYS* 4.6 12.0 - - - +
183B GLN* 5.0 5.4 + - - -
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Residues in contact with LEU 182 (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 THR* 3.5 9.1 + - - +
131A ALA* 2.8 32.4 + - + +
133A VAL* 4.9 2.5 - - + -
151A VAL* 4.2 6.7 - - + -
156A GLN* 4.8 3.8 - - - +
159A ASN* 4.2 17.0 - - - +
180A LEU* 3.9 16.8 - - + -
181A THR* 1.3 82.3 - - - +
183A SER* 1.3 69.2 + - - +
186A ASP* 4.5 16.4 - - + +
187A TYR* 4.6 12.3 - - + +
190A HIS* 5.4 2.0 - - + +
193A TYR* 3.5 40.8 - - + +
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Residues in contact with SER 183 (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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129A GLY 3.6 9.2 - - - -
130A THR* 4.4 3.4 - - - +
131A ALA* 3.8 1.8 - - - +
182A LEU* 1.3 80.2 - - - +
184A LYS* 1.3 62.8 + - - +
185A ALA* 3.3 6.9 + - - +
186A ASP* 2.6 49.1 + - - +
187A TYR* 3.1 18.0 + - - +
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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