Contacts of the helix formed by residues 556 - 565 (chain A) in PDB entry 4YCV
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 556 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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342A PHE* 5.9 4.7 - - - -
343A THR 4.3 2.7 - - - -
501A VAL* 3.0 19.4 + - - -
555A LEU* 1.3 74.9 - - - +
557A ILE* 1.3 49.4 + - - +
558A ASP* 2.6 4.5 + - - +
559A ARG* 2.5 47.0 + - - +
560A ILE* 3.3 12.6 + - - +
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Residues in contact with ILE 557 (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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254A ARG* 4.9 7.0 - - - +
257A ILE* 4.7 9.9 - - + -
258A ILE* 3.9 28.7 - - + -
261A LEU* 3.7 30.7 - - + -
325A ILE* 3.9 24.5 - - + -
343A THR* 3.6 24.2 + - + +
345A CYS* 4.0 15.3 - - + +
555A LEU* 3.5 6.6 - - + -
556A GLY* 1.3 72.6 - - - +
558A ASP* 1.3 52.7 + - - +
559A ARG 3.3 0.2 - - - -
560A ILE* 3.7 14.2 - - + +
561A THR* 2.7 46.4 + - - +
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Residues in contact with ASP 558 (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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254A ARG* 2.5 38.9 + - - +
327A LYS* 4.4 1.2 + - - -
342A PHE* 3.4 12.0 - - + +
343A THR* 2.6 34.1 + - - +
556A GLY 2.6 5.4 + - - +
557A ILE* 1.3 76.0 - - - +
559A ARG* 1.3 57.3 + - + +
561A THR* 3.4 0.5 + - - -
562A MET* 2.9 29.8 + - - +
570A ILE* 3.6 29.8 - - + -
573A VAL* 3.3 8.7 - - + +
574A ILE* 3.7 12.6 - - - +
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Residues in contact with ARG 559 (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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337A THR* 3.5 31.4 + - + +
338A HIS* 3.5 33.3 + - - -
499A LYS* 4.2 14.7 - - - +
500A GLU* 2.8 60.5 + - - +
501A VAL* 4.8 3.6 - - + -
556A GLY* 2.5 23.6 + - - +
558A ASP* 1.3 73.4 - - + +
560A ILE* 1.3 64.2 + - - +
562A MET* 3.0 22.1 + - - +
563A PHE* 3.0 39.5 + - + -
570A ILE* 5.1 2.5 - - + -
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Residues in contact with ILE 560 (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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257A ILE* 4.9 9.0 - - + -
364A PHE* 4.8 4.9 - - + -
365A PHE* 3.8 26.0 - - + -
368A LEU* 4.5 7.9 - - + -
496A ILE* 5.5 3.1 - - + -
501A VAL* 3.5 31.6 - - + -
555A LEU* 3.9 22.7 - - + -
556A GLY* 3.3 17.0 + - - +
557A ILE* 3.7 13.9 - - + +
559A ARG* 1.3 76.2 - - - +
561A THR* 1.3 58.6 + - - +
563A PHE* 3.3 8.3 + - - +
564A LEU* 2.9 55.4 + - + +
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Residues in contact with THR 561 (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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250A THR 4.6 1.1 - - - +
254A ARG* 3.7 41.6 - - + +
257A ILE* 3.8 17.8 - - + +
557A ILE* 2.7 27.0 + - - +
558A ASP* 3.5 6.5 - - - -
560A ILE* 1.3 74.1 - - - +
562A MET* 1.3 53.7 + - - +
565A THR* 2.4 59.5 + - + -
573A VAL* 3.8 18.4 - - + -
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Residues in contact with MET 562 (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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336A ASN 4.5 1.3 - - - +
337A THR* 4.5 16.4 - - + -
380A TYR* 4.5 5.6 - - - +
558A ASP 2.9 17.7 + - - +
559A ARG* 3.0 25.8 - - - +
561A THR* 1.3 75.7 - - - +
563A PHE* 1.3 66.8 + - + +
565A THR* 3.4 0.2 + - - -
566A ASN 3.0 8.7 + - - -
567A LYS 2.8 47.9 + - - +
568A ASN* 3.5 24.2 - - - +
569A SER 3.7 15.0 - - - +
570A ILE* 3.5 24.7 - - - -
573A VAL* 3.6 16.8 - - + +
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Residues in contact with PHE 563 (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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378A ILE* 3.9 15.2 - - + +
380A TYR* 3.5 49.3 - + + +
392A ILE* 5.0 1.8 - - + -
394A PHE* 5.6 0.9 - - + -
496A ILE* 3.4 50.7 - - + -
497A CYS* 3.4 26.0 - - + -
499A LYS* 4.7 12.8 - - + -
501A VAL* 4.1 13.7 - - + -
559A ARG* 3.0 34.4 + - + -
560A ILE* 3.3 5.8 + - - +
562A MET* 1.3 84.4 - - + +
564A LEU* 1.3 68.6 + - + +
566A ASN* 3.4 7.6 + - - +
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Residues in contact with LEU 564 (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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253A THR* 4.9 2.9 - - + +
257A ILE* 3.8 20.9 - - + -
365A PHE* 6.0 1.6 - - + -
368A LEU* 3.7 27.8 - - + -
369A VAL* 4.1 16.6 - - + -
372A LEU* 3.6 25.6 - - + -
373A PHE* 3.1 36.2 - - + -
378A ILE* 3.8 23.1 - - + -
394A PHE* 4.5 8.7 - - + -
496A ILE* 6.2 0.2 - - + -
560A ILE* 2.9 26.5 + - + +
563A PHE* 1.3 79.2 - - + +
565A THR* 1.3 60.2 + - - +
566A ASN* 3.3 1.8 - - - +
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Residues in contact with THR 565 (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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250A THR* 3.6 41.0 + - + +
253A THR* 3.7 24.0 - - + +
561A THR* 2.4 39.7 + - + +
562A MET 3.4 2.8 + - - -
564A LEU* 1.3 76.7 - - - +
566A ASN* 1.3 69.6 + - - +
567A LYS* 3.8 13.1 - - - +
573A VAL* 3.3 16.8 - - - +
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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