Contacts of the strand formed by residues 124 - 128 (chain G) 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 THR 124 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122G GLY 4.3 3.5 + - - -
123G ALA* 1.3 76.0 + - - +
125G ILE* 1.3 62.8 - - - +
149G SER* 3.3 22.9 + - - +
151G TYR* 3.7 29.6 - - + -
189G LYS 3.4 24.8 + - - +
190G ALA* 3.8 2.1 - - - -
191G ASP* 2.5 51.6 + - - +
192G LEU* 3.6 2.4 + - - +
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Residues in contact with ILE 125 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119G ILE* 4.1 18.2 - - + -
123G ALA* 4.7 3.6 - - + -
124G THR* 1.3 80.5 - - - +
126G LEU* 1.3 63.6 + - - +
127G THR* 4.1 11.0 - - - +
138G LEU* 3.6 30.3 - - + -
148G PHE* 4.1 17.0 - - + -
149G SER 3.0 9.1 + - - +
150G VAL* 3.2 12.7 - - + +
151G TYR* 2.7 34.6 + - - +
190G ALA* 5.3 0.2 - - - -
192G LEU* 3.5 18.8 - - + +
194G ILE* 3.7 35.7 - - + -
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Residues in contact with LEU 126 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124G THR 4.1 0.2 + - - -
125G ILE* 1.3 74.1 - - - +
127G THR* 1.3 78.7 + - - +
151G TYR* 3.3 23.8 - - + +
152G VAL* 4.6 1.6 - - - +
153G THR* 5.1 4.0 - - + -
178G VAL* 5.6 0.9 - - + -
183G VAL* 4.6 3.8 - - + -
186G ILE* 4.4 20.0 - - + -
187G MSE 3.6 19.7 - - + -
190G ALA* 3.9 16.8 - - + -
192G LEU 3.0 6.5 + - - -
193G VAL* 3.0 51.1 - - + +
194G ILE 3.2 5.5 + - - -
215G MSE 3.4 34.8 - - + -
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Residues in contact with THR 127 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125G ILE* 4.1 8.0 - - - +
126G LEU* 1.3 76.6 + - - +
128G HIS* 1.3 74.6 + - - +
129G ALA 4.8 3.4 - - - +
131G SER* 5.8 1.6 - - - -
134G VAL* 3.9 28.8 - - + +
138G LEU* 5.1 1.4 - - - +
150G VAL* 3.7 18.2 - - - +
151G TYR 2.7 8.9 + - - +
152G VAL* 3.2 28.6 - - - -
153G THR 3.4 4.0 + - - -
164G MSE 5.2 5.2 - - + +
194G ILE 2.8 25.6 + - - +
195G VAL* 4.5 1.8 - - + -
215G MSE 3.5 13.2 - - - +
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Residues in contact with HIS 128 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181F ALA* 5.1 2.5 - - + -
127G THR* 1.3 81.5 - - - +
129G ALA* 1.3 76.6 + - + +
130G TYR 3.8 2.9 + - - +
131G SER* 5.3 2.9 - - - -
153G THR* 2.6 25.9 + - + +
155G SER* 4.0 15.0 - - - -
180G ASP* 4.3 10.1 - - + -
195G VAL* 3.9 15.6 - - + +
208G ASN* 4.7 4.2 - - - +
209G LYS* 3.2 11.5 + - + +
210G ILE 3.0 27.5 + - - -
211G GLY* 4.0 10.1 - - - -
212G THR* 3.3 32.1 + - - +
215G MSE 3.4 24.5 - - + +
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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