Contacts of the helix formed by residues 303 - 311 (chain A) in PDB entry 3T79
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 PRO 303 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A VAL* 4.5 4.9 - - + -
91A ARG* 4.0 25.6 - - - +
279A PRO* 5.5 0.2 - - + -
281A PHE* 5.2 2.9 - - + -
297A GLU 3.6 8.3 - - - +
298A ASN* 3.9 12.2 - - + +
301A GLY 4.0 5.6 - - - +
302A ILE* 1.3 108.0 - - + +
304A ASP* 1.3 63.4 + - - +
305A PHE* 3.3 33.4 - - + -
306A TYR* 3.2 14.3 - - + +
307A ILE* 3.8 1.7 + - - +
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Residues in contact with ASP 304 (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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174A LYS* 4.2 6.4 + - - +
296A SER 3.1 24.8 - - - +
297A GLU* 2.9 19.2 + - - +
298A ASN 3.8 0.3 + - - -
299A THR* 2.9 39.3 + - - +
303A PRO* 1.3 68.6 - - - +
305A PHE* 1.3 68.5 + - - +
306A TYR 3.1 2.5 - - - -
307A ILE* 2.9 9.2 + - - +
308A GLU* 2.8 39.0 + - - +
315A LEU* 4.0 16.6 - - + +
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Residues in contact with PHE 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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51A VAL* 3.6 24.9 - - + -
52A LYS* 5.8 2.2 - - - -
55A ALA* 3.4 30.3 - - + -
95A LEU* 3.6 17.5 - - + -
98A LEU* 4.8 4.3 - - + -
99A LEU* 4.2 15.5 - - + -
303A PRO* 3.3 22.7 - - + -
304A ASP* 1.3 78.3 - - - +
306A TYR* 1.3 80.2 + + - +
308A GLU* 4.0 11.3 + - - +
309A LYS* 2.9 34.8 + - + +
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Residues in contact with TYR 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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51A VAL* 4.6 0.2 - - + -
91A ARG* 2.5 36.9 + - - -
94A GLY 4.6 1.5 - - - -
95A LEU* 3.7 28.1 + - + +
98A LEU* 3.2 32.1 - - + -
277A GLN 3.9 11.7 - - - -
278A PHE* 4.2 8.7 - + + -
279A PRO* 3.1 33.4 - - + +
302A ILE* 3.4 12.3 - - + -
303A PRO* 3.2 21.0 + - + +
305A PHE* 1.3 114.3 - + - +
307A ILE* 1.3 57.1 + - - +
309A LYS* 3.8 0.7 - - - +
310A MET* 3.0 36.4 + - - +
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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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186A VAL* 3.4 37.5 - - + +
188A VAL* 3.6 20.0 - - + -
278A PHE* 4.1 11.4 - - + -
299A THR* 2.7 43.1 - - + +
302A ILE* 4.3 9.2 - - + +
303A PRO 4.0 6.7 - - - +
304A ASP* 2.9 13.7 + - + +
306A TYR* 1.3 74.5 - - - +
308A GLU* 1.3 60.2 + - + +
311A ASN* 2.4 54.3 + - - +
315A LEU* 4.5 6.3 - - + -
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Residues in contact with GLU 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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304A ASP* 2.8 38.1 + - - +
305A PHE* 4.0 8.6 + - - +
307A ILE* 1.3 72.4 - - - +
309A LYS* 1.3 53.5 + - - +
311A ASN* 5.2 0.2 - - - -
312A ARG* 2.7 31.5 + - - -
313A THR 3.1 22.4 + - - +
314A LYS* 3.5 32.2 + - + +
315A LEU* 3.9 30.9 + - + +
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Residues in contact with LYS 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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98A LEU* 3.1 47.1 + - + +
99A LEU* 4.2 8.0 + - - +
101A PHE* 2.6 26.8 + - - -
102A ASP* 4.5 0.8 - - - +
103A TYR* 3.4 37.9 - - + +
276A PRO* 6.1 0.2 - - - -
305A PHE* 2.9 20.8 + - + +
306A TYR 3.8 2.7 - - - +
308A GLU* 1.3 78.5 - - - +
310A MET* 1.3 61.2 + - - +
312A ARG* 3.2 11.8 + - - +
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Residues in contact with MET 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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98A LEU* 3.4 24.7 - - + -
103A TYR* 3.7 25.1 + - - +
148A ASN* 3.3 31.9 - - - +
149A THR 3.8 14.4 - - - +
150A ASN* 4.9 0.7 - - + -
276A PRO* 4.4 4.9 - - + +
277A GLN* 3.6 24.9 - - - +
278A PHE* 3.4 59.7 - - + +
306A TYR* 3.0 18.1 + - - +
309A LYS* 1.3 76.3 - - - +
311A ASN* 1.3 64.7 + - - +
312A ARG* 3.3 3.5 + - - -
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Residues in contact with ASN 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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148A ASN* 3.6 24.9 + - - +
186A VAL 3.1 21.5 + - - +
187A LEU* 3.5 21.8 - - - +
188A VAL* 3.6 26.6 - - + +
190A ASN* 5.3 4.2 + - - +
278A PHE* 4.3 1.6 - - - -
307A ILE* 2.4 43.8 + - - +
308A GLU* 3.7 0.7 - - - -
310A MET* 1.3 81.4 - - - +
312A ARG* 1.3 73.9 + - - +
313A THR* 2.9 15.9 + - + +
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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