Contacts of the helix formed by residues 334 - 340 (chain A) in PDB entry 1Y1V
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 GLY 334 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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327A ALA 5.6 0.9 - - - -
328A ARG 3.2 13.9 - - - -
329A LEU 4.2 3.0 - - - +
330A LYS 3.9 10.8 - - - -
332A LYS 3.0 6.1 + - - -
333A GLU* 1.3 81.4 - - - +
335A ARG* 1.3 62.3 + - - -
336A ILE 2.9 3.9 + - - -
337A ARG* 3.1 3.3 + - - +
338A GLY* 2.5 33.9 + - - -
339A ASN* 4.2 2.9 - - - -
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Residues in contact with ARG 335 (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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328A ARG* 2.8 37.8 + - - +
329A LEU* 3.6 17.0 - - + -
334A GLY* 1.3 67.7 - - - -
336A ILE* 1.3 65.5 + - + +
339A ASN* 2.6 56.7 + - - +
340A LEU* 3.3 11.3 + - + +
1114B LEU* 4.2 16.1 - - - +
1115B THR* 5.3 2.4 + - - -
1199B ALA* 4.4 8.1 - - - +
1202B LEU* 3.5 23.6 - - - +
1203B LEU* 4.1 22.4 - - + +
1206B GLU* 2.2 60.9 + - - +
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Residues in contact with ILE 336 (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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329A LEU* 3.8 8.6 + - + +
334A GLY 2.9 4.4 + - - -
335A ARG* 1.3 79.9 - - - +
337A ARG* 1.3 63.6 + - + +
340A LEU* 3.5 12.2 - - + +
341A MET* 3.4 20.7 + - + +
1397A LEU* 5.7 0.4 - - + -
1400A CYS* 4.1 17.9 - - - +
1401A SER* 4.1 26.9 - - - -
1405A THR* 3.5 31.0 - - + +
1409A LEU* 5.3 0.4 - - + -
1429A ILE* 4.3 18.4 - - + -
1203B LEU* 3.4 45.5 - - + -
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Residues in contact with ARG 337 (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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329A LEU 4.6 2.6 + - - -
331A GLY* 4.0 13.1 - - - -
332A LYS* 3.2 58.3 - - - +
334A GLY 3.1 2.2 + - - -
336A ILE* 1.3 83.4 - - + +
338A GLY* 1.3 59.4 + - - +
339A ASN 3.7 0.2 - - - -
341A MET* 3.9 17.4 - - + +
342A GLY 4.0 2.1 + - - -
839A ARG* 2.5 38.0 - - - +
1401A SER 5.5 4.3 - - - +
1402A PHE* 5.6 0.2 - - - +
1403A GLU* 4.6 15.0 - - - +
1129B ARG* 3.5 12.7 + - - +
1132B GLU* 2.8 41.2 + - - +
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Residues in contact with GLY 338 (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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333A GLU* 4.2 8.7 - - - -
334A GLY 2.5 34.3 + - - +
337A ARG* 1.3 73.2 - - - +
339A ASN* 1.3 64.9 + - - +
342A GLY 2.8 17.7 - - - +
1117B GLN* 4.5 2.1 - - - +
1129B ARG* 2.8 23.1 + - - -
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Residues in contact with ASN 339 (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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333A GLU 5.7 0.9 - - - +
334A GLY* 4.6 1.3 - - - -
335A ARG* 2.6 59.1 + - - +
338A GLY* 1.3 82.4 - - - +
340A LEU* 1.3 62.3 + - - +
342A GLY 3.5 3.4 - - - -
343A LYS* 2.8 31.2 - - - +
1112B GLN* 5.1 1.9 - - - +
1115B THR* 4.2 17.5 + - - +
1117B GLN* 2.9 28.6 + - - +
1156B ASP* 3.9 0.2 - - - +
1199B ALA* 3.9 11.0 - - + +
1202B LEU* 5.5 0.6 - - - +
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Residues in contact with LEU 340 (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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335A ARG* 3.3 10.0 + - + +
336A ILE* 3.5 20.6 - - + +
339A ASN* 1.3 77.4 - - - +
341A MET* 1.3 62.6 + - - +
342A GLY* 3.1 5.5 + - - -
343A LYS* 4.4 6.0 - - - +
1428A VAL* 3.8 16.0 - - - +
1429A ILE* 3.8 41.7 - - + +
1151B LEU* 4.1 10.6 - - - +
1197B PRO* 3.7 21.8 - - + -
1199B ALA* 3.4 27.8 - - + -
1200B ALA* 3.6 14.8 - - - +
1203B LEU* 4.1 21.8 - - + -
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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