Contacts of the strand formed by residues 623 - 633 (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 HIS 623 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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599A TYR* 2.5 29.5 + - + +
600A THR 3.6 2.2 - - - -
601A TYR* 3.3 29.2 - + - -
621A PRO* 3.8 1.0 - - - +
622A LYS* 1.3 93.3 + - + +
624A MET* 1.3 68.1 + - - +
649A TYR* 4.3 15.7 - - + -
651A GLY* 2.9 29.4 + - - -
1101A DDQ 3.5 43.9 + - + -
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Residues in contact with MET 624 (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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75A GLY 4.2 2.5 - - - +
76A VAL 3.9 39.3 - - - +
77A SER* 4.2 13.2 - - - +
599A TYR* 3.6 3.3 - - - -
600A THR* 2.8 59.1 + - + +
602A THR* 4.5 8.1 - - - +
621A PRO* 3.4 30.5 - - + +
623A HIS* 1.3 78.8 - - - +
625A ALA* 1.3 66.5 + - - +
649A TYR* 3.4 17.7 - - - +
650A THR* 4.6 7.0 - - - -
651A GLY 4.8 0.9 - - - +
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Residues in contact with ALA 625 (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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598A SER* 3.3 17.7 - - - +
599A TYR* 3.9 4.9 - - + +
624A MET* 1.3 78.2 - - - +
626A SER* 1.3 61.9 + - - +
648A ARG* 3.6 0.2 - - - -
649A TYR* 2.4 53.9 + - + +
1101A DDQ 3.8 36.8 - - + -
1102A DDQ 4.8 1.1 - - + -
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Residues in contact with SER 626 (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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71A SER 3.4 15.7 + - - -
72A TYR* 3.2 31.1 - - - -
73A THR 4.4 0.2 + - - -
597A GLY* 4.1 0.2 - - - -
598A SER* 2.6 44.8 + - - +
625A ALA* 1.3 80.7 - - - +
627A LEU* 1.3 65.3 + - - +
647A GLY 3.0 12.6 - - - -
648A ARG* 4.0 8.5 - - - -
1101A DDQ 4.4 2.2 - - - +
1102A DDQ 4.5 3.1 - - - -
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Residues in contact with LEU 627 (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* 3.7 3.2 - - - -
595A VAL* 5.4 9.9 - - + -
596A VAL 3.7 12.6 - - - +
597A GLY* 3.9 10.1 - - - -
626A SER* 1.3 77.6 - - - +
628A TRP* 1.3 69.1 + - - +
629A ALA* 5.2 5.2 - - + +
646A GLY* 3.3 1.7 - - - -
647A GLY 2.8 39.2 + - - -
1101A DDQ 4.3 22.9 - - + -
1102A DDQ 4.6 9.0 - - + -
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Residues in contact with TRP 628 (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* 4.9 1.8 - + - -
60A LEU* 3.1 31.0 - - + -
61A HIS* 3.0 37.9 + + - -
72A TYR* 3.5 24.8 - - + -
594A ASN* 4.3 2.7 - - + -
595A VAL* 3.2 8.1 - - - +
596A VAL* 2.7 54.2 + - + +
627A LEU* 1.3 79.9 - - - +
629A ALA* 1.3 78.6 + - - +
630A ASP* 2.9 46.9 - - + -
644A GLY* 4.3 8.6 - - - -
645A THR* 3.3 22.0 + - - +
646A GLY* 3.5 13.2 - - - +
670A ASP* 5.1 4.1 + - + +
671A ALA* 5.8 0.8 - - - +
672A LEU* 4.4 9.9 - - + +
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Residues in contact with ALA 629 (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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593A VAL* 5.9 1.1 - - + -
594A ASN 3.3 4.9 - - - -
595A VAL* 3.7 16.8 - - + -
627A LEU* 5.2 5.6 - - + +
628A TRP* 1.3 80.2 - - - +
630A ASP* 1.3 62.6 + - - +
644A GLY* 3.1 2.4 - - - -
645A THR* 2.8 44.3 + - + +
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Residues in contact with ASP 630 (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* 2.4 32.4 + - - +
592A SER 3.6 0.3 - - - +
593A VAL* 3.3 7.3 - - - +
594A ASN* 2.6 75.7 + - - +
628A TRP* 2.9 33.5 - - + -
629A ALA* 1.3 74.7 - - - +
631A TYR* 1.3 62.2 + - - +
632A THR* 4.1 6.9 + - - -
642A THR* 4.2 8.3 - - + -
643A LEU 3.3 9.2 - - - +
644A GLY* 3.8 0.4 - - - -
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Residues in contact with TYR 631 (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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590A SER* 5.2 0.2 - - - -
592A SER* 3.0 23.5 + - - -
593A VAL* 3.0 32.3 - - + -
630A ASP* 1.3 75.1 - - - +
632A THR* 1.3 68.1 + - - +
633A PHE* 3.1 50.9 - + - -
635A ASP* 5.7 1.0 + - - -
641A LEU 3.7 1.7 - - - +
642A THR* 3.2 2.2 - - - -
643A LEU* 2.5 48.2 + - + +
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Residues in contact with THR 632 (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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20A SER* 3.6 21.3 + - - +
22A TRP* 3.9 3.7 - - + -
592A SER* 2.4 55.7 + - - -
594A ASN* 5.3 0.7 + - - -
630A ASP* 4.1 5.2 + - - -
631A TYR* 1.3 77.4 - - - +
633A PHE* 1.3 64.7 + - - +
634A PHE* 3.6 30.1 + - + -
640A GLY* 4.9 4.3 - - - -
641A LEU 3.6 9.6 - - - +
642A THR* 2.9 29.4 + - - +
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Residues in contact with PHE 633 (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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631A TYR* 3.1 37.7 - + - -
632A THR* 1.3 73.5 - - - +
634A PHE* 1.3 58.4 + - - +
635A ASP* 3.7 13.2 - - - +
638A LEU* 2.6 44.9 - - + +
639A SER* 3.0 1.9 - - - -
640A GLY* 2.5 35.0 + - - -
641A LEU* 3.0 37.6 + - + +
643A LEU* 4.3 12.6 - - + -
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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