Contacts of the helix formed by residues 240 - 252 (chain C) in PDB entry 4GKH
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 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 ARG* 4.6 11.1 + - - -
32A ASN* 3.8 6.6 - - - +
37A GLY 6.1 1.3 - - - -
38A ALA 6.2 0.2 - - - -
236C LEU 3.1 10.0 + - - +
239C PHE* 1.3 83.6 - - - +
241C PRO* 1.3 72.8 - - - +
242C SER* 2.8 23.9 + - - -
243C LEU* 3.0 15.6 + - - +
244C GLN* 3.1 20.3 + - - +
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Residues in contact with PRO 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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32A ASN* 3.6 20.2 - - - +
37A GLY* 6.4 2.5 - - - -
240C SER* 1.3 88.6 - - - +
242C SER* 1.3 56.2 + - - +
244C GLN* 3.3 19.6 + - + +
245C LYS* 2.9 29.9 + - - +
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Residues in contact with SER 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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37A GLY* 4.9 14.9 + - - -
118C GLU* 5.2 5.0 + - - -
240C SER* 2.8 20.3 + - - -
241C PRO* 1.3 82.2 - - - +
243C LEU* 1.3 59.0 + - - +
245C LYS* 3.5 8.2 + - - +
246C ARG* 2.9 29.0 + - - +
249C GLN* 5.3 0.2 - - - +
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Residues in contact with LEU 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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30A ARG* 4.4 13.0 - - - +
110C LEU* 4.6 7.6 - - + -
117C GLY* 3.5 42.0 - - - +
118C GLU* 3.9 21.5 - - + +
121C VAL* 3.6 19.0 - - + +
236C LEU* 3.9 23.1 - - + +
239C PHE* 4.2 20.9 - - + -
240C SER* 3.0 23.9 + - - +
242C SER* 1.3 76.4 + - - +
244C GLN* 1.3 65.9 + - - +
246C ARG* 3.3 7.5 + - - +
247C LEU 3.1 17.7 + - - -
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Residues in contact with GLN 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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32A ASN* 5.5 1.0 + - - -
6B ARG* 5.8 0.2 - - - +
233C TRP* 2.9 86.5 + - + +
234C ASN* 4.6 0.8 - - - +
236C LEU* 3.8 8.5 - - + +
237C GLY* 3.3 30.3 - - - +
240C SER 3.1 7.2 + - - +
241C PRO* 3.4 24.7 - - - +
243C LEU* 1.3 78.1 - - - +
245C LYS* 1.3 63.0 + - - +
247C LEU* 3.3 15.6 + - - +
248C PHE* 3.8 3.6 + - - -
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Residues in contact with LYS 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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159A GLY 3.0 29.3 + - - -
160A LEU* 4.0 20.7 + - - +
161A VAL 5.7 0.4 + - - -
233C TRP* 5.5 0.7 - - - +
241C PRO 2.9 17.4 + - - +
242C SER* 3.7 7.9 - - - +
244C GLN* 1.3 76.0 - - - +
246C ARG* 1.3 63.0 + - - +
248C PHE* 3.2 10.8 + - - +
249C GLN* 3.1 51.1 + - + +
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Residues in contact with ARG 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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118C GLU* 3.3 46.8 + - - +
119C ASN* 5.5 2.0 + - - -
121C VAL* 4.0 8.3 - - + -
122C ASP* 2.7 41.9 + - - +
242C SER 2.9 17.5 + - - +
243C LEU* 3.7 9.0 - - - +
244C GLN 3.3 0.2 - - - -
245C LYS* 1.3 74.3 - - - +
247C LEU* 1.3 60.6 + - - +
249C GLN* 3.6 15.9 - - + +
250C LYS* 2.8 31.7 + - + +
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Residues in contact with LEU 247 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121C VAL* 3.6 11.2 - - + +
125C ALA* 4.0 23.0 - - + +
128C LEU* 5.2 2.2 - - + -
229C LEU* 3.9 30.5 - - + +
232C LEU* 3.6 32.1 - - + -
233C TRP* 3.8 35.2 - - + +
236C LEU* 4.0 9.2 - - + -
243C LEU 3.1 11.5 + - - +
244C GLN 3.4 10.3 - - - +
245C LYS 3.2 0.2 - - - -
246C ARG* 1.3 76.3 - - - +
248C PHE* 1.3 63.0 + - + +
250C LYS* 3.9 0.5 - - - -
251C TYR* 3.0 30.5 + - + +
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Residues in contact with PHE 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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226C TYR* 3.6 28.0 - + - -
229C LEU* 3.9 28.0 - - + -
233C TRP* 3.3 39.7 - + + -
244C GLN 3.9 4.7 - - - -
245C LYS* 3.2 9.1 + - - +
247C LEU* 1.3 80.9 - - + +
249C GLN* 1.3 61.4 + - + +
251C TYR* 3.7 3.7 - - - +
252C GLY 2.8 25.1 + - - -
253C ILE* 2.9 36.5 + - + +
256C PRO* 3.7 36.6 - - + -
261C LEU* 3.8 23.1 - - + -
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Residues in contact with GLN 249 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245C LYS* 3.1 49.7 + - + +
246C ARG* 3.6 20.7 - - + +
248C PHE* 1.3 77.5 - - + +
250C LYS* 1.3 63.0 + - - +
252C GLY* 3.3 12.0 + - - -
253C ILE 4.7 5.8 - - - +
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Residues in contact with LYS 250 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121C VAL 5.2 0.4 - - - +
122C ASP* 3.8 41.5 + - - +
125C ALA* 3.6 23.2 - - + -
126C VAL* 4.0 23.1 - - + -
129C ARG* 5.5 1.0 - - - +
246C ARG* 2.8 21.6 + - + +
249C GLN* 1.3 71.5 - - - +
251C TYR* 1.3 66.4 + - - +
252C GLY* 3.3 1.6 + - - -
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Residues in contact with TYR 251 (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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125C ALA* 3.9 17.4 - - + +
128C LEU* 3.9 17.9 - - + -
129C ARG* 2.8 78.1 + - + +
132C HIS* 2.6 36.3 + + - +
225C ARG* 2.9 28.8 + - - -
229C LEU* 3.9 18.2 - - + -
247C LEU* 3.0 19.7 + - + +
248C PHE* 3.8 6.1 - - - +
250C LYS* 1.3 76.6 - - - +
252C GLY* 1.3 58.7 + - - +
253C ILE* 3.7 30.3 - - + -
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Residues in contact with GLY 252 (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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129C ARG* 4.2 8.3 + - - -
248C PHE 2.8 9.6 + - - -
249C GLN* 3.7 9.9 - - - -
250C LYS 3.1 3.0 - - - -
251C TYR* 1.3 79.9 - - - +
253C ILE* 1.3 62.3 + - - +
254C ASP* 4.0 7.7 + - - +
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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