Contacts of the strand formed by residues 149 - 153 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123E ALA 3.1 9.6 + - - +
124E THR* 4.4 17.0 - - - +
125E ILE* 2.8 26.1 + - - +
148E PHE* 1.3 74.4 - - - +
150E VAL* 1.3 74.5 + - - +
151E TYR* 5.3 4.0 - - - -
174E PRO* 3.7 20.2 + - - +
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Residues in contact with VAL 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125E ILE* 3.2 20.0 - - + +
127E THR* 4.4 9.9 - - + +
138E LEU* 4.3 13.7 - - + -
148E PHE* 3.9 23.3 - - + -
149E SER* 1.3 85.5 + - - +
151E TYR* 1.3 81.1 + - - +
152E VAL* 4.4 1.3 - - + +
168E LEU* 3.8 24.7 - - + -
173E VAL* 4.2 6.1 - - + -
174E PRO 3.0 13.5 + - - +
175E VAL* 3.3 7.8 - - + +
176E THR* 2.9 26.7 + - - -
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Residues in contact with TYR 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269D GLU* 3.5 6.6 + - - -
124E THR* 3.8 29.6 - - + -
125E ILE 2.7 7.9 + - - +
126E LEU* 3.2 22.7 - - + +
127E THR 2.9 25.6 + - - -
149E SER* 5.3 4.0 - - - -
150E VAL* 1.3 77.9 - - - +
152E VAL* 1.3 60.9 + - - +
176E THR* 3.5 38.8 - - + -
178E VAL* 3.9 8.7 - - + -
186E ILE* 3.4 35.2 - - + -
189E LYS* 3.3 36.5 + - + +
190E ALA* 5.2 5.6 - - + -
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Residues in contact with VAL 152 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126E LEU* 4.6 0.2 - - - -
127E THR* 3.3 27.4 - - - +
129E ALA 3.5 22.2 - - - +
150E VAL* 4.7 2.9 - - + -
151E TYR* 1.3 74.3 - - - +
153E THR* 1.3 77.2 + - - +
161E GLY 3.7 20.4 - - - +
164E MSE 4.3 6.7 - - + -
165E ALA* 4.2 5.2 - - + +
168E LEU* 5.4 0.2 - - + -
175E VAL* 4.1 18.4 - - + -
176E THR 3.1 10.5 + - - +
177E VAL* 3.4 10.5 - - + +
178E VAL* 3.2 22.8 + - - +
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Residues in contact with THR 153 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126E LEU* 5.0 1.1 - - + +
127E THR 3.5 1.8 + - - -
128E HIS* 2.5 32.5 + - + +
129E ALA 3.3 7.8 + - - -
152E VAL* 1.3 77.5 - - - +
154E GLU* 1.3 64.3 + - - +
155E SER 3.4 0.2 + - - -
161E GLY* 3.2 17.5 - - - -
177E VAL* 4.8 0.2 - - - -
178E VAL* 3.2 14.8 - - + -
180E ASP* 4.0 21.1 - - + -
183E VAL* 3.3 34.5 - - + -
215E MSE 3.7 12.6 - - + -
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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