Contacts of the strand formed by residues 641 - 650 (chain A) in PDB entry 1QFG
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 641 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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631A TYR 3.7 1.7 - - - +
632A THR* 3.6 0.7 - - - -
633A PHE* 3.0 56.4 + - + +
638A LEU* 3.5 38.0 + - + +
640A GLY* 1.3 77.5 - - - +
642A THR* 1.3 64.9 + - - +
643A LEU* 3.7 25.6 - - + -
673A VAL* 5.3 4.9 - - + -
674A ARG 3.3 14.1 - - - +
675A TYR* 4.2 14.1 - - + -
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Residues in contact with THR 642 (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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22A TRP* 3.6 25.2 - - + -
60A LEU* 4.7 2.2 - - + -
630A ASP* 4.2 10.5 - - + -
631A TYR 3.2 11.7 - - - +
632A THR* 2.9 30.3 + - - +
640A GLY 4.1 1.8 + - - -
641A LEU* 1.3 72.8 + - - +
643A LEU* 1.3 78.7 - - - +
672A LEU* 4.6 9.6 - - + -
673A VAL* 3.2 5.2 - - - +
674A ARG* 2.6 48.7 + - - +
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Residues in contact with LEU 643 (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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630A ASP* 3.3 1.4 - - - -
631A TYR* 2.5 48.0 + - + +
633A PHE* 4.3 15.9 - - + -
641A LEU* 3.7 31.6 - - + -
642A THR* 1.3 81.0 - - - +
644A GLY* 1.3 56.9 + - - +
672A LEU 3.5 1.8 - - - -
673A VAL* 3.1 39.0 - - + -
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Residues in contact with GLY 644 (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 TRP* 4.3 12.1 - - - -
629A ALA 3.1 12.1 - - - -
630A ASP* 3.8 4.9 - - - -
643A LEU* 1.3 77.1 - - - +
645A THR* 1.3 67.2 + - - -
671A ALA* 3.2 3.5 - - - +
672A LEU* 2.9 37.9 + - - +
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Residues in contact with THR 645 (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 TRP* 3.3 8.4 - - - +
629A ALA* 2.8 35.8 + - + +
644A GLY* 1.3 79.1 - - - -
646A GLY* 1.3 58.1 + - - +
669A VAL* 4.2 11.3 - - - +
670A ASP 3.0 15.8 + - - -
671A ALA* 3.6 9.9 - - - +
694A LEU* 5.0 1.9 - - - +
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Residues in contact with GLY 646 (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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72A TYR* 4.0 6.3 - - - -
627A LEU 3.3 12.1 - - - -
628A TRP* 3.5 12.9 - - - -
645A THR* 1.3 78.3 + - - +
647A GLY* 1.3 58.9 + - - -
648A ARG* 6.0 0.2 - - - -
668A VAL 3.9 0.2 - - - +
669A VAL* 3.2 10.2 - - - +
670A ASP* 2.6 37.7 + - - +
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Residues in contact with GLY 647 (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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72A TYR* 4.2 1.4 + - - -
626A SER* 3.0 6.1 - - - -
627A LEU 2.8 41.2 + - - +
646A GLY* 1.3 76.3 - - - -
648A ARG* 1.3 63.7 + - - -
667A THR* 5.1 2.5 - - - -
668A VAL 3.4 5.8 - - - -
669A VAL* 4.5 6.7 - - - -
1102A DDQ 3.5 16.6 - - - +
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Residues in contact with ARG 648 (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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68A GLU* 6.6 0.7 - - - -
71A SER* 3.6 34.8 + - - +
72A TYR* 3.9 18.3 + - - +
78A VAL* 5.4 5.8 - - - +
625A ALA 3.6 2.2 - - - +
626A SER* 4.0 15.9 - - - -
646A GLY 5.8 0.4 + - - -
647A GLY* 1.3 77.0 - - - -
649A TYR* 1.3 60.7 + - - +
650A THR* 3.8 2.8 + - - +
666A TYR* 3.7 4.0 - - - +
667A THR* 3.1 8.2 - - - +
668A VAL* 2.8 62.2 + - + +
670A ASP* 2.4 33.5 + - - -
692A ASN* 5.8 0.8 - - - +
699A TYR* 5.3 3.2 + - - -
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Residues in contact with TYR 649 (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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623A HIS* 4.0 8.1 - - + -
624A MET* 3.4 9.6 - - - +
625A ALA* 2.4 59.5 + - + +
647A GLY 4.0 0.8 - - - -
648A ARG* 1.3 72.4 - - - +
650A THR* 1.3 62.4 + - - +
651A GLY* 3.7 20.8 - - - -
665A SER* 3.4 24.4 - - - -
666A TYR 3.4 6.1 - - - -
667A THR* 3.1 23.3 - - - +
1101A DDQ 3.2 41.5 - - + -
1102A DDQ 3.0 68.7 - - + -
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Residues in contact with THR 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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77A SER* 6.5 1.1 - - - -
621A PRO* 4.4 15.9 - - + -
623A HIS 4.6 0.2 - - - -
624A MET* 4.6 8.3 - - + +
648A ARG* 3.8 3.5 + - - +
649A TYR* 1.3 77.6 + - - +
651A GLY* 1.4 68.3 + - - +
653A SER* 6.5 0.2 - - - -
665A SER* 2.9 5.7 - - - -
666A TYR* 2.7 87.4 + - + +
701A ALA 5.1 1.6 - - - +
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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