Contacts of the strand formed by residues 149 - 153 (chain F) in PDB entry 3ECS
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 SER 149 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122F GLY 5.3 0.7 + - - -
123F ALA 3.2 3.6 + - - +
124F THR* 3.4 25.9 + - - +
125F ILE* 2.8 25.5 + - - +
148F PHE* 1.3 75.3 - - - +
150F VAL* 1.3 69.0 + - - +
174F PRO* 3.4 23.3 - - - -
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Residues in contact with VAL 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124F THR* 5.2 0.2 - - - -
125F ILE* 3.3 18.2 - - + +
127F THR* 4.0 15.3 - - + -
138F LEU* 4.5 7.4 - - + -
148F PHE* 4.0 13.9 - - + -
149F SER* 1.3 83.4 - - - +
151F TYR* 1.3 76.7 + - - +
152F VAL* 4.5 0.7 - - + +
168F LEU* 4.0 26.9 - - + -
173F VAL* 3.9 20.2 - - + -
174F PRO 2.8 12.2 + - - +
175F VAL* 3.1 7.8 - - + -
176F THR* 2.8 30.8 + - - -
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Residues in contact with TYR 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124F THR* 3.7 32.1 - - + -
125F ILE 2.9 6.9 + - - +
126F LEU* 3.4 19.5 - - + +
127F THR 3.0 24.1 + - - -
149F SER* 6.5 0.4 - - - -
150F VAL* 1.3 76.0 - - - +
152F VAL* 1.3 60.8 + - - +
176F THR* 3.2 31.4 - - + +
178F VAL* 3.9 11.0 - - + -
186F ILE* 3.4 28.0 - - + -
189F LYS* 3.1 39.7 + - + +
190F ALA* 5.5 3.8 - - + -
267G LYS* 3.9 7.8 + - - -
269G GLU* 3.6 15.5 + - - -
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Residues in contact with VAL 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126F LEU* 4.9 0.4 - - - -
127F THR* 3.3 26.2 - - + +
129F ALA 3.5 25.6 - - - +
150F VAL* 4.7 2.9 - - + -
151F TYR* 1.3 74.6 - - - +
153F THR* 1.3 73.0 + - - +
161F GLY* 3.7 21.8 - - - +
164F MSE 4.3 5.6 - - + -
165F ALA* 4.0 19.3 - - + +
168F LEU* 5.6 0.4 - - + -
175F VAL* 4.1 7.2 - - + -
176F THR 3.0 13.6 + - - +
177F VAL* 3.4 4.8 - - + -
178F VAL* 3.1 23.0 + - - +
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Residues in contact with THR 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126F LEU* 5.1 2.0 - - + -
127F THR 3.4 2.8 + - - +
128F HIS* 2.5 31.4 + - + +
129F ALA 3.3 6.9 + - - -
152F VAL* 1.3 77.0 - - - +
154F GLU* 1.3 65.1 + - - +
155F SER* 3.0 1.0 + - - -
161F GLY* 3.1 17.3 - - - -
178F VAL* 3.2 11.7 - - + +
179F LEU 4.3 2.9 - - - +
180F ASP* 3.3 20.6 - - - +
183F VAL* 3.2 34.8 - - + -
215F MSE 3.6 14.4 - - + -
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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