Contacts of the strand formed by residues 479 - 486 (chain A) in PDB entry 4C2M
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 ALA 479 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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476A VAL* 4.2 8.9 + - + +
477A ASN 3.5 4.7 - - - +
478A TYR* 1.3 79.5 - - - +
480A ALA* 1.3 64.4 + - - +
505A LEU* 3.8 11.1 - - - +
634A ASN* 6.1 0.2 - - + -
635A MET 3.0 15.5 - - - +
636A HIS* 3.4 27.6 - - + +
637A PHE 4.7 0.4 - - - +
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Residues in contact with ALA 480 (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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479A ALA* 1.3 78.0 - - - +
481A ARG* 1.3 59.8 + - - +
501A PHE* 3.8 41.7 - - + -
505A LEU* 5.0 8.5 - - + -
634A ASN* 3.2 6.8 - - - +
635A MET* 2.7 42.0 + - + +
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Residues in contact with ARG 481 (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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480A ALA* 1.3 76.9 - - - +
482A SER* 1.3 66.8 + - - +
501A PHE* 3.6 11.3 - - - -
592A GLN* 3.3 30.5 - - - +
614A LEU* 5.4 0.4 - - - -
632A GLU* 2.7 59.6 + - + +
633A MET 3.3 10.7 + - - +
634A ASN* 2.9 24.2 + - - +
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Residues in contact with SER 482 (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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481A ARG* 1.3 79.2 - - - +
483A VAL* 1.3 78.4 + - - +
484A ILE 3.6 0.2 + - - -
501A PHE* 3.9 13.0 - - - -
612A LYS 4.0 4.4 + - - -
613A THR* 3.5 10.6 - - - +
614A LEU* 3.4 31.1 + - - +
632A GLU* 3.2 6.9 - - - -
633A MET 2.9 31.3 + - - +
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Residues in contact with VAL 483 (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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482A SER* 1.3 90.3 + - - +
484A ILE* 1.3 75.8 + - - +
485A SER* 4.7 4.7 - - - +
613A THR* 3.2 24.2 - - + -
614A LEU 3.3 3.8 + - - -
630A GLY* 4.0 28.7 - - - +
631A ASP 3.6 9.4 - - - +
632A GLU* 4.1 13.9 - - + +
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Residues in contact with ILE 484 (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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482A SER 4.3 0.2 - - - +
483A VAL* 1.3 87.8 - - - +
485A SER* 1.3 63.8 + - - +
495A ILE* 5.7 0.4 - - + -
589A MET* 5.3 1.1 - - + -
614A LEU* 3.3 20.6 - - + +
616A LEU* 4.1 11.4 - - + -
626A ALA* 3.8 26.9 - - + -
628A PHE* 3.8 35.7 - - + +
630A GLY 5.4 0.2 + - - -
631A ASP* 3.2 28.2 + - - +
633A MET* 3.7 46.2 - - + +
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Residues in contact with SER 485 (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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483A VAL* 4.7 2.1 - - - +
484A ILE* 1.3 75.6 + - - +
486A PRO* 1.3 70.5 - - - +
613A THR* 2.7 31.5 + - - +
614A LEU 2.8 6.6 + - - -
615A ARG* 3.3 30.5 + - - -
616A LEU 3.0 24.3 + - - -
628A PHE* 3.4 5.4 - - - -
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Residues in contact with PRO 486 (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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485A SER* 1.3 88.4 - - - +
487A ASP* 1.3 60.3 + - - +
488A PRO* 4.6 1.9 - - - +
615A ARG* 3.3 26.5 + - - +
616A LEU 3.5 7.2 - - - +
618A TYR* 3.5 38.6 - - + +
628A PHE* 3.4 29.1 - - + -
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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