Contacts of the helix formed by residues 238 - 243 (chain D) in PDB entry 6GL7
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 LEU 238 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B TYR* 3.3 44.2 - - + +
182D ILE* 4.3 16.4 - - + +
185D CYS* 3.6 19.1 - - + +
186D ASN* 3.6 40.2 - - + +
194D ARG* 5.4 2.7 - - - +
204D LEU* 6.1 1.3 - - + -
235D GLN* 3.0 15.0 + - - +
236D THR 4.3 4.7 - - - +
237D ILE* 1.3 79.2 - - - +
239D PRO* 1.3 72.3 - - - +
240D SER* 3.0 10.1 - - - +
241D CYS* 2.8 18.9 + - + +
242D SER 2.9 10.4 + - - -
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Residues in contact with PRO 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D ARG* 3.0 46.9 - - + +
235D GLN* 3.5 23.1 - - - +
237D ILE 3.6 1.3 - - - -
238D LEU* 1.3 86.9 - - - +
240D SER* 1.3 55.5 + - - +
241D CYS 2.8 6.4 + - - -
242D SER* 4.2 1.1 - - - +
243D TYR* 3.2 19.9 + - + +
244D GLU* 2.7 47.0 + - + +
308D ASN* 3.6 13.9 - - - +
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Residues in contact with SER 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194D ARG* 3.8 38.3 + - - +
195D CYS* 4.8 0.2 - - - -
235D GLN* 5.1 6.8 + - - +
238D LEU* 3.0 10.9 + - - +
239D PRO* 1.3 77.6 - - - +
241D CYS* 1.3 56.8 + - - +
244D GLU* 3.5 23.4 + - - +
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Residues in contact with CYS 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185D CYS 3.0 20.4 - - - +
194D ARG* 5.1 2.7 - - + -
195D CYS* 2.0 51.0 - - + -
197D ARG* 3.2 27.0 - - - +
200D CYS* 3.5 30.3 - - - -
238D LEU* 2.8 13.6 + - + +
239D PRO 2.8 0.4 + - - -
240D SER* 1.3 80.3 + - - +
242D SER* 1.3 60.0 + - - +
243D TYR 3.5 1.1 - - - -
244D GLU 4.1 4.7 - - - +
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Residues in contact with SER 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D ARG* 2.9 11.1 + - - -
200D CYS* 3.8 9.4 - - - -
201D HIS* 2.8 33.9 + - - -
204D LEU* 3.4 28.0 - - - -
237D ILE* 2.6 38.4 + - - +
238D LEU 2.9 5.2 + - - -
239D PRO* 4.2 0.3 - - - +
241D CYS* 1.3 78.1 - - - +
243D TYR* 1.3 60.7 + - - +
306D THR* 4.4 6.4 - - - +
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Residues in contact with TYR 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197D ARG* 3.0 11.5 + - - +
234D ARG* 4.8 7.2 - - - -
239D PRO* 3.2 11.0 + - + -
241D CYS 3.5 0.2 - - - -
242D SER* 1.3 79.6 + - - +
244D GLU* 1.3 73.0 - - + +
248D LYS* 6.0 0.3 - - - -
306D THR* 3.3 20.6 - - + -
307D PRO 4.1 0.4 - - - -
308D ASN* 3.3 44.2 + - + +
309D TYR 4.6 8.2 + - - -
310D VAL* 5.5 3.6 - - - +
320D SER* 2.7 30.4 + - - -
321D PRO 2.7 34.4 + - - -
322D TRP* 3.0 54.1 - + + +
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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