Contacts of the strand formed by residues 670 - 675 (chain A) in PDB entry 1QFM
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 LEU 670 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A TYR* 2.9 19.4 + - + +
630A TYR* 4.4 5.4 - - + -
631A PRO 3.6 23.1 - - - +
633A MET* 3.5 27.1 - - + -
653A ILE* 3.6 14.4 - - + +
656A LEU* 3.7 31.2 - - + +
657A GLN* 3.0 26.8 + - + +
660A VAL* 4.0 13.7 - - + -
661A GLY* 3.7 21.5 - - - +
666A GLN* 4.2 11.0 - - + +
668A ASN 3.9 4.0 - - - +
669A PRO* 1.3 76.3 - - - +
671A LEU* 1.3 59.7 + - - +
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Residues in contact with LEU 671 (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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4A PHE* 3.8 28.9 - - + -
6A TYR* 4.2 0.7 - - + -
46A GLN* 5.5 0.4 - - - +
49A ILE* 4.0 15.7 - - + -
50A THR* 3.4 24.7 - - + +
53A PHE* 3.7 40.4 - - + -
54A LEU* 5.5 0.2 - - + -
633A MET 2.9 11.0 + - - +
634A LEU* 3.3 12.4 - - + -
635A LEU* 2.8 23.8 + - - +
653A ILE* 3.7 10.8 - - - +
657A GLN* 4.5 1.6 - - - +
669A PRO* 4.1 10.3 - - + -
670A LEU* 1.3 83.3 - - - +
672A ILE* 1.3 61.4 + - - +
699A PHE* 4.0 13.7 - - + -
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Residues in contact with ILE 672 (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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42A PHE* 5.3 0.7 - - + -
46A GLN* 3.5 39.6 + - + +
47A ASN* 3.9 4.0 - - - +
50A THR* 2.7 27.4 + - - -
634A LEU* 4.5 0.4 - - - -
635A LEU* 3.2 18.2 - - + +
637A THR* 4.1 2.7 - - + -
649A SER* 3.8 37.9 - - - +
650A LEU* 3.9 21.3 - - + -
653A ILE* 3.9 17.9 - - + +
671A LEU* 1.3 76.6 - - - +
673A HIS* 1.3 68.6 + - - +
674A VAL* 3.9 12.3 - - + -
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Residues in contact with HIS 673 (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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47A ASN* 3.3 16.5 + - - -
50A THR* 4.0 13.2 - - + +
51A VAL* 3.8 28.7 - - + +
54A LEU* 5.0 4.0 - - + -
634A LEU* 4.7 0.9 - - + -
635A LEU 2.9 7.7 + - - +
636A LEU* 3.6 22.3 - - + -
637A THR 3.1 26.0 + - - +
672A ILE* 1.3 75.3 - - - +
674A VAL* 1.3 70.9 + - - +
675A ASP* 4.6 21.7 + - + +
695A ASP* 3.9 22.2 + - - -
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Residues in contact with VAL 674 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A VAL* 3.8 35.2 - - + +
47A ASN* 2.9 25.9 + - - +
637A THR* 3.4 11.7 - - + +
638A ALA* 4.1 5.4 - - - -
639A ASP* 3.9 20.4 - - + +
646A PRO* 5.4 3.1 - - + -
650A LEU* 4.0 11.9 - - + -
672A ILE* 3.9 27.6 - - + -
673A HIS* 1.3 79.2 - - - +
675A ASP* 1.3 70.3 + - - +
676A THR* 5.0 4.0 - - + +
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Residues in contact with ASP 675 (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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637A THR 2.9 15.7 + - - +
638A ALA* 4.1 9.6 - - + -
639A ASP* 3.0 27.7 + - - +
673A HIS* 4.0 18.3 + - + +
674A VAL* 1.3 77.6 - - - +
676A THR* 1.3 75.1 + - - +
678A ALA* 3.6 6.7 - - + +
684A LYS* 5.2 5.5 + - - +
688A LYS* 2.9 41.0 + - - +
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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