Contacts of the helix formed by residues 299 - 316 (chain B) in PDB entry 4C8B
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 GLU 299 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A ASN* 5.1 7.9 - - - +
157A GLU* 4.9 2.6 - - - +
310A LYS* 3.1 30.9 + - - +
123B ARG* 5.3 1.2 + - - -
297B PHE 3.4 3.2 + - - -
298B GLU* 1.3 71.4 - - - +
300B ILE* 1.3 63.4 + - - +
302B PHE* 3.1 39.7 + - + +
303B LEU* 3.9 14.6 + - - +
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Residues in contact with ILE 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A ILE* 3.7 20.2 - - + -
310A LYS* 3.3 39.3 - - + +
311A LYS* 3.7 30.3 - - + +
314A LEU* 6.1 1.1 - - + -
298B GLU* 4.4 12.3 - - + +
299B GLU* 1.3 80.0 + - - +
301B THR* 1.3 72.4 + - - +
302B PHE 3.2 0.7 + - - -
303B LEU* 3.3 7.2 + - - +
304B GLU* 3.1 31.7 + - - +
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Residues in contact with THR 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B PRO* 3.1 35.9 - - + -
297B PHE* 4.8 5.2 - - + -
298B GLU* 2.9 28.2 + - - +
300B ILE* 1.3 84.1 - - - +
302B PHE* 1.3 59.7 + - - +
304B GLU* 3.5 14.5 + - + +
305B ALA* 3.1 21.7 + - - +
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Residues in contact with PHE 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B PRO* 3.2 45.8 - - + -
120B LEU* 4.0 2.4 - - - +
123B ARG* 3.6 44.2 - - + +
294B LEU* 4.0 24.9 - - + -
297B PHE* 3.8 23.1 - + + -
298B GLU 4.5 0.2 - - - -
299B GLU* 3.1 45.4 + - + +
301B THR* 1.3 75.2 - - - +
303B LEU* 1.3 68.3 + - + +
305B ALA* 3.1 8.3 + - - +
306B VAL* 3.0 26.9 + - - +
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Residues in contact with LEU 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A GLU* 3.4 36.6 - - + +
303A LEU* 3.5 33.2 - - + +
306A VAL* 4.7 10.8 - - + -
307A ILE* 3.4 20.2 - - + +
310A LYS* 4.3 22.4 - - + -
123B ARG* 4.4 6.1 - - - +
157B GLU* 5.1 1.8 - - + -
299B GLU* 3.9 20.2 - - - +
300B ILE* 3.3 5.3 + - - +
302B PHE* 1.3 80.5 - - - +
304B GLU* 1.3 57.0 + - - +
306B VAL* 3.2 8.0 + - + +
307B ILE* 2.9 35.6 + - + +
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Residues in contact with GLU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A ILE* 3.7 13.7 - - + -
311A LYS* 3.3 28.9 + - - +
300B ILE* 3.1 29.6 + - - +
301B THR* 3.8 16.0 + - + +
303B LEU* 1.3 76.7 - - - +
305B ALA* 1.3 63.4 + - - +
307B ILE* 3.3 8.8 + - + +
308B GLN* 3.0 23.7 + - - +
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Residues in contact with ALA 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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117B ALA* 3.7 31.3 + - + +
119B PRO* 5.0 1.1 - - + -
120B LEU* 3.9 25.7 - - + +
301B THR 3.1 14.3 + - - +
302B PHE 3.1 8.7 + - - +
304B GLU* 1.3 76.8 - - - +
306B VAL* 1.3 63.6 + - - +
308B GLN* 3.4 6.8 + - - +
309B LEU* 3.2 24.1 + - - +
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Residues in contact with VAL 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A LEU* 4.8 11.0 - - + -
120B LEU* 4.1 22.7 - - + -
123B ARG* 4.2 5.2 - - - +
157B GLU* 3.7 27.1 - - + +
158B PHE* 3.7 27.1 - - + -
302B PHE 3.0 14.8 + - - +
303B LEU* 3.2 10.5 + - + +
305B ALA* 1.3 73.9 - - - +
307B ILE* 1.3 67.2 + - + +
309B LEU* 3.2 9.0 + - - +
310B LYS* 3.1 34.2 + - + +
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Residues in contact with ILE 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ILE* 5.5 3.1 - - + +
303A LEU* 3.1 57.2 - - + +
304A GLU* 5.0 10.1 - - + +
307A ILE* 4.9 13.9 - - + -
303B LEU* 2.9 22.7 + - + +
304B GLU* 3.6 10.1 - - + +
306B VAL* 1.3 75.0 - - - +
308B GLN* 1.3 64.9 + - - +
310B LYS* 3.3 7.2 + - + +
311B LYS* 2.9 55.2 + - + +
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Residues in contact with GLN 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B GLU 3.0 13.8 + - - +
305B ALA* 3.7 10.5 - - - +
306B VAL 3.2 0.2 - - - -
307B ILE* 1.3 78.5 - - - +
309B LEU* 1.3 63.7 + - - +
311B LYS* 3.2 7.4 + - - +
312B THR* 2.9 31.8 + - + +
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Residues in contact with LEU 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B LEU* 4.1 7.6 - - + -
113B TYR* 3.8 28.2 - - + -
115B ASP 3.3 27.1 + - - +
116B VAL* 4.0 13.5 - - + -
117B ALA 5.9 0.7 - - - +
120B LEU* 3.5 29.4 - - + -
158B PHE* 3.8 34.5 - - + -
305B ALA 3.2 13.8 + - - +
306B VAL* 3.2 8.0 + - - +
308B GLN* 1.3 76.9 - - - +
310B LYS* 1.3 59.4 + - - +
312B THR* 3.1 8.8 + - - +
313B LYS* 2.8 31.3 + - - +
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Residues in contact with LYS 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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299A GLU* 3.5 34.3 + - - +
300A ILE* 5.6 12.3 - - + -
303A LEU* 4.1 19.3 - - + +
100B ASN* 4.5 6.5 - - - +
156B ASN* 2.7 38.4 + - - +
158B PHE* 4.1 22.4 - - + -
306B VAL* 3.1 24.6 + - + +
307B ILE* 3.9 4.9 - - + +
309B LEU* 1.3 79.8 - - - +
311B LYS* 1.3 63.2 + - + +
313B LYS* 3.6 11.1 + - + +
314B LEU* 3.0 24.8 + - - +
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Residues in contact with LYS 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ILE* 5.6 8.5 - - + -
304A GLU* 3.9 20.3 + - - +
307B ILE* 2.9 42.9 + - + +
308B GLN* 3.5 7.4 - - - +
310B LYS* 1.3 76.6 - - + +
312B THR* 1.3 53.2 + - + +
314B LEU* 3.3 3.8 + - - +
315B GLN* 2.6 40.9 + - + +
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Residues in contact with THR 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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112B GLU 4.1 3.5 + - - -
113B TYR* 5.0 1.6 - - - -
114B PRO* 3.9 25.3 - - + +
115B ASP* 5.4 7.0 + - + +
308B GLN* 2.9 24.7 + - + +
309B LEU* 3.1 13.7 + - - +
311B LYS* 1.3 73.3 - - + +
313B LYS* 1.3 63.1 + - - +
315B GLN* 4.9 1.8 - - - -
316B SER* 2.7 44.9 + - - +
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Residues in contact with LYS 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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100B ASN* 5.5 5.2 - - - +
112B GLU* 3.4 47.1 - - + +
113B TYR* 3.9 20.9 - - + +
158B PHE* 6.1 1.1 - - + -
309B LEU 2.8 16.9 + - - +
310B LYS* 3.8 12.1 - - + +
312B THR* 1.3 79.4 + - - +
314B LEU* 1.3 58.0 + - - +
316B SER 4.0 10.1 - - - +
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Residues in contact with LEU 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 LYS 3.0 18.1 + - - +
311B LYS* 3.7 4.0 - - - +
313B LYS* 1.3 75.8 - - - +
315B GLN* 1.3 63.7 + - - +
316B SER 3.3 6.8 + - - +
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Residues in contact with GLN 315 (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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311B LYS* 2.6 23.4 + - + +
312B THR* 4.9 1.3 - - - -
314B LEU* 1.3 73.7 - - - +
316B SER* 1.3 57.2 + - - +
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Residues in contact with SER 316 (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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111B THR 5.4 7.6 - - - -
112B GLU 6.0 1.1 - - - -
114B PRO* 5.6 6.7 - - - -
312B THR* 2.7 32.3 + - - -
313B LYS 4.0 8.8 - - - +
314B LEU 3.7 8.1 - - - +
315B GLN* 1.3 76.0 - - - +
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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
------------------------------------------------------------
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