Contacts of the strand formed by residues 649 - 653 (chain A) in PDB entry 1N1M
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 CYS 649 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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624A ILE 4.2 0.6 + - - -
625A ALA* 3.4 25.1 - - - -
626A ILE* 3.2 24.5 + - - +
640A LEU* 4.2 9.2 - - - +
647A PHE* 3.5 1.4 - - - +
648A LYS* 1.3 77.3 - - - +
650A GLY* 1.3 59.8 + - - +
699A GLU* 3.1 24.9 - - + +
758A PHE* 4.1 10.5 - - + -
759A ILE* 4.8 3.4 - - - -
762A CYS* 2.0 50.3 - - + -
763A PHE* 4.4 1.1 - - - -
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Residues in contact with GLY 650 (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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625A ALA* 5.3 0.9 - - - -
626A ILE* 2.8 15.3 - - - -
640A LEU* 3.4 19.6 - - - +
649A CYS* 1.3 77.6 - - - +
651A ILE* 1.3 65.2 + - - -
699A GLU 2.9 7.9 + - - +
700A TYR* 3.5 5.7 - - - -
701A LEU 3.0 23.4 + - - -
758A PHE* 3.7 3.8 - - - -
759A ILE* 5.8 0.7 - - - -
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Residues in contact with ILE 651 (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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563A TRP* 4.4 4.0 - - + -
626A ILE 3.0 5.1 + - - -
627A TRP* 3.0 31.6 - - + +
628A GLY 3.2 6.5 + - - +
636A THR* 3.5 5.0 - - - +
650A GLY* 1.3 73.6 - - - -
652A ALA* 1.3 63.5 + - - +
653A VAL* 4.3 2.5 - - + -
701A LEU* 3.4 24.7 - - + +
703A ILE* 4.1 6.5 - - + -
755A MET* 3.1 47.1 - - + +
758A PHE* 3.4 34.8 - - + -
759A ILE* 3.7 25.6 - - + -
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Residues in contact with ALA 652 (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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628A GLY 3.8 4.0 - - - -
633A GLY* 3.7 14.6 - - - +
636A THR* 4.5 2.5 - - + -
637A SER* 3.3 26.2 - - - +
651A ILE* 1.3 74.0 - - - +
653A VAL* 1.3 62.2 + - - +
655A PRO* 4.1 8.3 - - + -
700A TYR* 3.7 18.1 - - + +
701A LEU 2.9 8.2 + - - +
702A LEU* 3.8 2.4 - - + +
703A ILE* 2.9 28.2 + - - +
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Residues in contact with VAL 653 (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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627A TRP* 4.3 8.3 - - + -
628A GLY 3.1 8.3 + - - +
629A TRP* 3.3 45.6 - - + +
630A SER 2.8 22.3 + - - -
633A GLY* 4.3 0.6 - - - -
651A ILE* 4.3 0.7 - - + -
652A ALA* 1.3 74.2 - - - +
654A ALA* 1.3 69.5 + - + +
655A PRO* 3.2 3.2 - - - +
703A ILE* 3.4 11.4 - - + +
742A ILE* 4.0 17.0 - - + -
751A ILE* 4.0 11.0 - - + -
755A MET* 3.3 33.9 - - + -
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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