Contacts of the strand formed by residues 300 - 304 (chain A) in PDB entry 3H44
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 GLN 300 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296A GLU 3.5 13.3 + - - +
297A HIS* 3.2 27.6 + - - +
298A LEU 2.9 17.0 - - - +
299A LYS* 1.3 85.7 - - - +
301A LEU* 1.3 60.0 + - - +
302A TYR* 3.5 28.6 - - + +
476A VAL 3.8 3.2 + - - -
477A ARG* 3.9 2.1 - - + +
478A VAL 3.0 27.1 + - - +
502A GLN* 3.0 30.8 + - - +
503A GLU 3.5 11.0 + - - -
504A ALA* 4.2 10.1 - - - +
505A ILE* 3.6 6.5 - - - +
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Residues in contact with LEU 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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300A GLN* 1.3 74.9 - - - +
302A TYR* 1.3 80.8 + - - +
303A LYS* 3.9 21.4 + - + +
478A VAL* 3.4 22.4 - - + +
480A ILE* 3.9 23.6 - - + -
501A LYS 3.8 0.3 - - - +
502A GLN* 3.4 5.4 - - - +
503A GLU* 2.7 61.6 + - + +
505A ILE* 3.9 18.4 - - + +
506A PRO* 6.2 2.5 - - + -
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Residues in contact with TYR 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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204A LEU* 5.5 0.2 - - + -
208A THR* 3.6 27.2 + - + -
297A HIS* 5.1 1.2 - - - -
300A GLN* 3.5 31.3 - - + +
301A LEU* 1.3 75.4 - - - +
303A LYS* 1.3 62.9 + - - +
304A ILE* 4.0 21.3 - - + +
477A ARG* 2.9 44.5 + - + -
478A VAL 2.9 20.6 + - - +
479A ALA* 3.4 1.8 - - + +
480A ILE 2.8 27.5 + - - +
500A TYR* 4.1 18.4 - + + -
501A LYS 3.3 5.2 - - - +
502A GLN* 3.6 36.1 + - + -
2002A DIO 3.6 16.2 - - - -
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Residues in contact with LYS 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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301A LEU* 3.9 21.9 - - + +
302A TYR* 1.3 75.0 - - - +
304A ILE* 1.3 60.6 + - - +
480A ILE* 3.6 8.3 - - + -
485A PHE* 3.6 45.1 - - + -
489A THR* 4.1 3.3 - - + +
500A TYR* 3.1 7.6 - - - +
501A LYS* 2.9 52.0 + - + +
503A GLU* 2.8 38.7 + - - +
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Residues in contact with ILE 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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201A LEU* 4.1 15.5 - - + -
204A LEU* 3.2 30.5 - - + -
302A TYR* 4.1 10.3 - - + -
303A LYS* 1.3 80.4 - - - +
305A VAL* 1.3 68.9 + - - +
306A PRO 4.0 0.2 - - - -
479A ALA* 4.0 26.2 - - + -
480A ILE 2.8 14.8 + - - +
481A VAL* 3.3 16.2 - - + -
482A SER 2.9 31.1 + - - +
485A PHE* 3.5 2.6 - - - -
498A THR* 3.7 28.3 - - + -
499A GLN 3.7 3.8 - - - +
500A TYR* 4.0 5.8 - - + -
2002A DIO 4.3 7.0 - - - -
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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