Contacts of the strand formed by residues 140 - 145 (chain A) in PDB entry 3L6D
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 HIS 140 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A ILE* 3.9 3.3 - - - +
128A VAL* 2.9 35.5 + - + +
138A GLU 3.4 16.5 + - - -
139A SER* 1.3 74.3 - - - +
141A SER* 1.3 62.1 + - - +
161A ALA* 3.7 2.9 - - - -
163A HIS* 3.2 46.9 + + + +
164A THR* 5.6 1.8 - - - -
165A VAL* 6.3 2.0 - - + -
213B GLU* 3.5 24.8 + - + +
214B THR* 3.7 48.2 + - + +
217B PHE* 5.5 4.2 - - + +
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Residues in contact with SER 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A TYR* 5.1 2.9 - - - -
126A MSE 3.3 12.1 - - - -
127A ILE* 4.1 11.0 - - - -
128A VAL* 4.4 0.9 - - - +
140A HIS* 1.3 78.5 - - - +
142A ILE* 1.3 67.0 + - - +
143A HIS* 3.2 16.5 - - - -
157A LEU 5.0 2.8 + - - -
160A LEU* 6.4 0.2 - - - -
161A ALA* 3.9 14.7 + - - +
163A HIS 2.9 6.2 + - - -
164A THR* 2.7 29.4 + - - -
165A VAL* 3.2 24.8 + - - +
214B THR* 5.5 0.3 - - - +
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Residues in contact with ILE 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A GLY* 3.4 2.9 - - - -
126A MSE 2.8 59.1 + - + +
128A VAL* 4.4 8.7 - - + -
141A SER* 1.3 77.7 - - - +
143A HIS* 1.3 68.0 + - - +
165A VAL* 3.5 21.3 - - + +
167A LEU* 4.6 7.4 - - + -
172A ALA* 4.2 21.3 - - + +
175A PHE* 3.7 28.0 - - + -
176A ALA* 4.2 17.0 - - + -
179A LEU* 3.9 19.5 - - + -
180A HIS* 5.4 0.7 - - + -
214B THR* 4.8 3.8 - - + -
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Residues in contact with HIS 143 (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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98A VAL* 4.2 1.8 - - + -
100A TYR* 2.8 30.8 + - - -
123A VAL* 3.8 16.4 - - + -
124A LYS 3.2 7.2 - - - +
125A GLY* 3.5 17.9 - - - -
126A MSE 4.7 0.4 - - - -
141A SER* 3.2 27.8 - - - -
142A ILE* 1.3 77.4 - - - +
144A THR* 1.3 63.5 + - - +
150A PHE* 3.6 26.0 - + + -
157A LEU* 3.6 24.1 - - + +
164A THR* 3.0 19.2 + - - -
165A VAL 2.8 11.3 + - - +
166A PHE* 3.3 7.5 - - + -
167A LEU 3.0 24.9 + - - -
172A ALA* 4.4 0.2 - - - +
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Residues in contact with THR 144 (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 VAL* 3.4 10.0 - - - +
124A LYS* 2.9 56.0 + - + +
126A MSE 4.5 2.2 - - + -
143A HIS* 1.3 73.3 - - - +
145A GLY* 1.3 65.8 + - - +
146A ASP 3.8 0.2 + - - -
166A PHE* 3.5 11.2 - - - -
167A LEU 2.7 21.4 + - - -
168A PRO* 3.3 0.5 - - - +
169A TRP* 3.1 37.9 + - + +
172A ALA* 3.5 18.4 - - + -
173A LEU* 5.4 1.3 - - + -
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Residues in contact with GLY 145 (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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112A GLN* 3.5 28.0 + - - -
122A TYR 3.6 6.1 - - - -
144A THR* 1.3 81.5 + - - +
146A ASP* 1.3 60.3 + - - -
147A ARG* 3.4 2.0 + - - +
166A PHE* 3.4 12.5 - - - -
169A TRP* 4.0 10.3 - - - +
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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