Contacts of the helix formed by residues 299 - 314 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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297A PHE 3.5 3.3 + - - -
298A GLU* 1.3 72.2 - - - +
300A ILE* 1.3 64.0 + - - +
301A THR 3.2 0.3 + - - -
302A PHE* 3.2 33.6 + - + +
303A LEU* 3.9 9.9 + - - +
156B ASN* 3.7 19.2 + - - +
310B LYS* 3.5 38.6 + - - +
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Residues in contact with ILE 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A GLU* 3.2 3.4 + - + +
299A GLU* 1.3 80.6 + - - +
301A THR* 1.3 63.4 + - + +
302A PHE 3.1 0.7 + - - -
303A LEU* 3.2 10.4 + - - +
304A GLU* 3.1 36.5 + - + +
307B ILE* 6.1 2.9 - - + +
310B LYS* 5.6 13.0 - - + -
311B LYS* 5.6 10.5 - - + +
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Residues in contact with THR 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A PRO* 3.9 25.7 - - + +
297A PHE* 4.0 9.6 - - + +
298A GLU* 2.7 38.0 + - + +
300A ILE* 1.3 78.5 - - + +
302A PHE* 1.3 62.7 + - - +
304A GLU* 3.8 17.9 - - - +
305A ALA* 3.0 23.0 + - - +
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Residues in contact with PHE 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A PRO* 3.2 46.4 - - + -
120A LEU* 4.2 3.0 - - - +
123A ARG* 3.9 39.7 - - + +
294A LEU* 4.0 23.6 - - + -
297A PHE* 3.6 32.1 - + + -
298A GLU 4.5 0.7 - - - -
299A GLU* 3.2 31.3 + - + +
300A ILE 3.2 0.8 - - - -
301A THR* 1.3 77.2 + - - +
303A LEU* 1.3 67.5 + - + +
305A ALA* 3.2 7.3 + - - +
306A VAL* 3.0 27.8 + - - +
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Residues in contact with LEU 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A ARG* 5.0 2.9 - - - +
157A GLU* 5.4 0.9 - - + -
299A GLU* 3.9 22.9 - - - +
300A ILE* 3.2 11.3 + - - +
302A PHE* 1.3 85.8 - - + +
304A GLU* 1.3 56.1 + - - +
306A VAL* 3.2 7.6 + - + +
307A ILE* 2.9 30.3 + - - +
156B ASN* 4.8 0.9 - - - +
157B GLU* 4.0 28.7 - - + +
303B LEU* 3.5 28.0 - - + -
306B VAL* 4.8 7.6 - - + -
307B ILE* 3.1 32.0 - - + +
310B LYS* 4.1 20.0 - - + +
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Residues in contact with GLU 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ILE* 3.1 30.6 + - + +
301A THR* 3.8 18.9 - - - +
303A LEU* 1.3 72.9 - - - +
305A ALA* 1.3 66.7 + - - +
307A ILE* 3.2 13.5 - - + +
308A GLN* 3.1 24.6 + - - +
307B ILE* 5.0 13.5 - - + -
311B LYS* 3.9 22.3 + - - +
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Residues in contact with ALA 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A ALA* 3.7 31.1 + - + +
119A PRO* 5.0 1.3 - - + -
120A LEU* 3.9 26.4 - - + +
301A THR 3.0 14.1 + - - +
302A PHE 3.2 9.2 + - - +
304A GLU* 1.3 76.8 - - - +
306A VAL* 1.3 63.1 + - - +
308A GLN* 3.5 5.8 + - - +
309A LEU* 3.3 23.7 + - - +
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Residues in contact with VAL 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A LEU* 4.1 17.5 - - + -
123A ARG* 4.1 13.0 - - - +
157A GLU* 3.7 24.9 - - + +
158A PHE* 3.8 24.2 - - + -
302A PHE 3.0 14.6 + - - +
303A LEU* 3.2 10.5 + - + +
305A ALA* 1.3 74.6 - - - +
307A ILE* 1.3 67.2 + - - +
309A LEU* 3.2 7.4 + - - +
310A LYS* 3.1 38.7 + - + +
303B LEU* 4.7 9.4 - - + -
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Residues in contact with ILE 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A LEU 2.9 18.3 + - - +
304A GLU* 3.2 23.3 - - + +
306A VAL* 1.3 73.9 - - - +
308A GLN* 1.3 70.7 + - - +
310A LYS* 3.3 4.9 + - - +
311A LYS* 3.0 51.1 + - - +
300B ILE* 3.7 23.8 - - + -
303B LEU* 3.4 33.6 - - + +
304B GLU* 3.7 19.5 - - + +
307B ILE* 4.9 11.2 - - + -
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Residues in contact with GLN 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ASP* 6.0 6.5 - - + +
304A GLU 3.1 17.8 + - - +
305A ALA* 3.6 7.0 - - - +
307A ILE* 1.3 79.8 - - - +
309A LEU* 1.3 64.3 + - - +
311A LYS* 3.2 23.7 + - - +
312A THR* 2.9 47.6 + - + +
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Residues in contact with LEU 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A LEU* 4.1 7.9 - - + -
113A TYR* 3.8 25.0 - - + -
115A ASP 3.3 26.9 + - - +
116A VAL* 4.0 13.5 - - + -
117A ALA 5.9 0.7 - - - +
120A LEU* 3.5 29.6 - - + -
158A PHE* 3.7 34.3 - - + -
305A ALA 3.3 12.2 + - - +
306A VAL 3.2 7.9 + - - +
308A GLN* 1.3 79.3 - - - +
310A LYS* 1.3 57.9 + - - +
312A THR* 3.1 8.5 + - - +
313A LYS* 2.8 32.5 + - - +
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Residues in contact with LYS 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ASN* 4.5 6.9 + - - +
156A ASN* 2.8 32.9 + - - +
157A GLU* 4.7 0.4 - - - +
158A PHE* 4.1 15.3 - - + -
306A VAL* 3.1 32.3 + - + +
307A ILE* 3.8 3.1 - - - +
309A LEU* 1.3 79.0 - - - +
311A LYS* 1.3 61.1 + - - +
313A LYS* 3.8 9.9 - - + +
314A LEU* 3.0 26.0 + - - +
299B GLU* 3.1 32.6 + - - +
300B ILE* 3.3 23.5 - - + +
303B LEU* 4.3 22.1 - - + +
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Residues in contact with LYS 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A ILE* 3.0 37.9 + - - +
308A GLN* 3.5 24.3 + - - +
310A LYS* 1.3 80.2 - - - +
312A THR* 1.3 64.2 + - + +
314A LEU* 3.5 9.7 + - - +
315A GLN* 3.6 17.5 - - - +
300B ILE* 3.7 14.8 - - + -
304B GLU* 3.3 27.6 + - - +
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Residues in contact with THR 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A GLU 3.6 12.6 + - - -
113A TYR* 4.6 2.3 - - - -
114A PRO* 3.9 21.8 - - + +
115A ASP* 5.6 1.9 + - + -
308A GLN* 2.9 39.7 + - + +
309A LEU* 3.1 12.5 + - - +
311A LYS* 1.3 73.1 - - + +
313A LYS* 1.3 69.5 + - - +
315A GLN* 2.9 19.8 + - - +
316A SER* 3.3 12.0 + - - -
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Residues in contact with LYS 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A PRO 3.9 6.6 + - - -
100A ASN* 2.8 40.7 + - - +
112A GLU* 3.2 30.4 + - - +
113A TYR* 2.8 35.9 + - + +
158A PHE* 5.2 2.7 - - + -
309A LEU 2.8 20.1 + - - +
310A LYS* 3.8 9.0 - - + +
312A THR* 1.3 73.5 + - - +
314A LEU* 1.3 57.7 + - - +
315A GLN 2.9 5.5 + - - -
316A SER* 3.2 17.9 + - - +
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Residues in contact with LEU 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A LYS 3.0 18.0 + - - +
311A LYS* 3.9 6.7 - - - +
312A THR 3.2 0.6 - - - -
313A LYS* 1.3 76.8 - - - +
315A GLN* 1.3 70.4 + - + +
316A SER 3.5 0.8 + - - -
300B ILE* 6.1 1.3 - - + -
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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