Contacts of the helix formed by residues 304 - 314 (chain B) in PDB entry 1C1D
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 304 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298B ARG* 3.9 11.7 - - - +
302B GLY 3.7 1.4 + - - -
303B TRP* 1.4 78.0 - - - +
305B GLU* 1.3 66.2 + - - +
306B SER* 3.4 8.5 + - - -
307B VAL* 3.2 26.1 + - - +
308B VAL* 2.9 22.3 + - - +
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Residues in contact with GLU 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B LEU* 5.3 8.8 - - - +
146B ALA 5.4 2.3 - - - +
294B HIS* 5.6 5.3 - - + -
298B ARG* 3.5 37.2 + - - +
304B SER* 1.3 75.7 - - - +
306B SER* 1.3 58.3 + - - +
308B VAL* 3.3 6.3 + - - +
309B HIS* 3.0 48.3 + - + +
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Residues in contact with SER 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304B SER* 3.2 8.6 + - - -
305B GLU* 1.3 80.5 - - - +
307B VAL* 1.3 63.4 + - - +
309B HIS* 3.4 6.8 + - - +
310B GLU* 3.1 23.5 + - - +
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Residues in contact with VAL 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B TRP* 3.7 21.1 - - + -
304B SER* 3.2 24.7 + - - +
306B SER* 1.3 76.9 - - - +
308B VAL* 1.3 68.0 + - - +
310B GLU* 3.2 20.6 + - - +
311B ARG* 3.0 54.4 + - - +
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Residues in contact with VAL 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B THR* 3.6 18.6 - - + +
293B ILE* 3.9 18.5 - - + +
294B HIS* 3.5 31.9 - - + +
298B ARG* 3.6 25.4 - - + +
303B TRP* 4.1 16.4 - - + -
304B SER 2.9 19.5 + - - +
305B GLU* 3.7 5.8 - - - +
307B VAL* 1.3 79.7 - - - +
309B HIS* 1.3 61.2 + - + +
311B ARG* 3.2 7.8 + - - +
312B ALA* 2.9 27.5 + - - +
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Residues in contact with HIS 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B PHE* 4.1 27.3 - + - -
152B THR* 3.3 35.8 + - + -
155B VAL* 4.5 10.8 - - + +
294B HIS* 5.7 0.6 + - - -
305B GLU* 3.0 36.7 + - + +
306B SER* 3.4 7.1 + - - +
307B VAL 3.2 0.2 - - - -
308B VAL* 1.3 77.4 - - + +
310B GLU* 1.3 57.1 + - - +
312B ALA* 3.2 4.9 + - - +
313B VAL* 2.9 34.2 + - + +
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Residues in contact with GLU 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306B SER 3.1 13.3 + - - +
307B VAL* 3.6 25.5 - - - +
308B VAL 3.2 0.2 - - - -
309B HIS* 1.3 78.9 - - - +
311B ARG* 1.3 85.1 + - + +
313B VAL* 3.2 10.5 + - - +
314B ALA* 3.0 24.9 + - - +
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Residues in contact with ARG 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B ILE* 3.7 27.6 - - + +
303B TRP* 3.1 43.6 - - + +
307B VAL* 3.0 38.7 + - - +
308B VAL 3.2 4.2 + - - +
310B GLU* 1.3 91.6 + - - +
312B ALA* 1.3 66.0 + - - +
314B ALA* 3.1 23.2 + - - +
315B ILE* 3.6 3.5 + - - +
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Residues in contact with ALA 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B THR* 3.7 33.7 - - + +
155B VAL* 4.3 5.6 - - + -
156B GLY* 3.8 15.2 - - - +
159B GLU* 4.5 0.5 - - - +
290B GLY* 4.4 5.4 - - - -
293B ILE* 4.1 11.4 - - + +
308B VAL 2.9 13.5 + - - +
309B HIS* 3.2 8.3 + - - +
311B ARG* 1.3 77.4 - - - +
313B VAL* 1.4 62.2 + - - +
315B ILE* 3.0 24.3 + - - +
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Residues in contact with VAL 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B VAL* 4.1 11.7 - - + -
159B GLU* 3.8 43.8 - - + +
309B HIS* 2.9 21.6 + - + +
310B GLU* 3.2 11.9 + - - +
312B ALA* 1.4 77.4 - - - +
314B ALA* 1.3 58.3 + - - +
315B ILE 3.0 5.8 + - - -
316B GLY* 3.1 12.1 + - - -
317B ASP 4.5 0.5 + - - -
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Residues in contact with ALA 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B GLU 3.0 13.2 + - - +
311B ARG* 3.1 19.9 + - - +
313B VAL* 1.3 72.3 - - - +
315B ILE* 1.3 64.0 + - - +
316B GLY 3.0 2.5 - - - -
317B ASP* 3.0 14.2 + - + +
318B THR* 3.0 24.0 + - - +
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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