Contacts of the helix formed by residues 240 - 248 (chain C) in PDB entry 4S10
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 PRO 240 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A SER* 4.6 0.2 - - - -
53A ARG* 4.0 7.9 - - - +
100A LEU 3.5 14.1 - - - +
101A HIS 3.6 17.7 - - - +
102A ARG 4.4 4.7 - - - +
103A PRO* 3.9 17.3 - - + -
198C HIS* 3.4 28.3 - - + +
234C SER* 3.9 12.8 - - - -
238C THR 4.2 0.2 - - - +
239C GLU* 1.3 89.3 - - + +
241C GLU* 1.3 66.6 + - - +
242C ALA 4.1 0.4 - - - +
243C MET* 3.0 30.1 + - + +
244C LEU* 3.3 9.9 + - - +
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Residues in contact with GLU 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A VAL* 5.1 1.6 - - + -
28A THR* 3.2 28.3 - - - +
29A PHE* 3.1 11.8 + - - +
30A SER* 2.7 48.6 + - - +
31A SER 4.0 3.5 + - - +
32A PHE* 3.7 32.0 - - + +
53A ARG* 4.9 0.2 - - - -
100A LEU* 3.4 22.3 + - + +
102A ARG 5.5 0.6 + - - -
239C GLU 3.6 2.0 + - - -
240C PRO* 1.3 70.7 - - - +
242C ALA* 1.3 57.0 + - - +
244C LEU* 3.2 4.2 + - - -
245C GLN* 2.8 46.5 + - + +
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Residues in contact with ALA 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A LEU* 2.8 30.6 + - + +
101A HIS* 3.5 38.6 - - + +
193C LEU* 4.5 3.5 - - + +
198C HIS* 4.2 3.6 - - + +
241C GLU* 1.3 77.6 - - - +
243C MET* 1.3 62.2 + - - +
245C GLN* 3.4 17.3 + - - +
246C VAL* 3.4 18.2 + - - +
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Residues in contact with MET 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180C TRP* 3.7 20.0 - - + -
183C PHE* 4.1 10.1 - - + -
191C LEU* 4.0 19.3 - - + -
193C LEU* 5.2 0.7 - - - -
198C HIS* 3.8 35.8 - - + +
200C TRP* 3.7 27.4 - - + -
234C SER* 4.3 2.7 - - - -
239C GLU* 3.9 5.6 - - + -
240C PRO* 3.0 30.6 + - + +
242C ALA* 1.3 73.9 - - - +
244C LEU* 1.3 63.9 + - + +
246C VAL* 3.3 2.1 + - - +
247C LEU* 2.9 57.2 + - + +
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Residues in contact with LEU 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A PHE* 3.3 41.8 - - + -
30A SER* 3.7 25.1 - - - +
180C TRP* 4.0 15.7 - - + -
239C GLU* 4.0 20.9 - - + +
240C PRO 3.3 8.9 + - - +
241C GLU* 3.2 7.9 + - - +
243C MET* 1.3 73.8 - - - +
245C GLN* 1.3 59.8 + - - +
248C GLY* 2.8 45.4 + - - +
249C PRO* 4.3 1.8 - - + -
250C LYS* 3.9 18.6 - - + +
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Residues in contact with GLN 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A GLN 4.0 17.2 + - - +
2A VAL* 3.6 13.1 - - + +
27A ARG* 2.8 31.5 + - - +
29A PHE* 3.9 13.6 - - - -
100A LEU* 5.3 6.1 - - + -
241C GLU* 2.8 37.0 + - + +
242C ALA* 3.4 14.6 - - - +
243C MET 3.2 0.2 - - - -
244C LEU* 1.3 77.9 - - - +
246C VAL* 1.3 61.2 + - + +
248C GLY* 4.4 1.7 + - - -
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Residues in contact with VAL 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C GLN* 3.4 27.1 - - + +
178C VAL* 4.1 20.4 - - + -
191C LEU* 4.4 9.4 - - + -
193C LEU* 4.2 22.4 - - + -
242C ALA 3.4 12.1 + - - +
243C MET 3.3 7.0 + - - +
244C LEU 3.2 0.2 - - - -
245C GLN* 1.3 82.5 - - + +
247C LEU* 1.3 68.4 + - + +
248C GLY 3.3 1.0 + - - -
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Residues in contact with LEU 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C LEU* 5.4 0.2 - - + -
178C VAL* 3.8 19.3 - - + +
179C SER* 3.7 37.2 - - - +
180C TRP* 3.1 42.3 + - + +
183C PHE* 3.9 17.3 - - + -
191C LEU* 4.2 10.8 - - + -
243C MET* 2.9 45.6 + - + +
246C VAL* 1.3 81.6 - - + +
248C GLY* 1.3 59.7 + - - +
249C PRO* 4.8 0.2 - - - +
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Residues in contact with GLY 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A PHE* 4.3 7.4 - - - -
180C TRP* 2.9 17.5 + - - -
244C LEU* 2.8 29.3 + - - +
245C GLN 4.3 1.9 + - - -
246C VAL 3.3 2.8 + - - -
247C LEU* 1.3 80.6 - - - +
249C PRO* 1.3 70.7 - - - +
250C LYS 3.5 0.7 + - - -
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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