Contacts of the helix formed by residues 614 - 624 (chain A) in PDB entry 1QU2
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 GLY 614 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A LEU* 3.9 11.7 - - - -
21A PRO* 4.5 1.6 - - - -
24A GLU* 3.6 8.5 - - - -
609A VAL* 2.9 8.9 + - - +
610A VAL* 2.9 22.8 + - - -
613A LYS* 1.3 79.1 - - - +
615A ALA* 1.3 66.9 + - - -
616A ASP 3.3 2.0 - - - -
617A ILE* 3.2 5.1 + - - +
618A ALA 3.2 15.1 + - - -
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Residues in contact with ALA 615 (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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24A GLU* 2.7 19.7 + - - +
141A ARG* 3.3 28.3 - - - +
142A LEU* 3.9 12.9 - - - +
610A VAL* 4.2 13.1 - - + +
614A GLY* 1.3 71.2 - - - -
616A ASP* 1.3 64.0 + - - +
618A ALA* 3.0 6.6 + - - +
619A ARG* 2.9 26.8 + - - +
762A HIS* 3.7 16.4 - - + -
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Residues in contact with ASP 616 (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 LEU* 4.2 10.5 - - + -
24A GLU* 2.9 10.7 + - - +
614A GLY 3.3 0.2 - - - -
615A ALA* 1.3 77.0 - - - +
617A ILE* 1.3 57.6 + - - +
619A ARG* 3.5 6.8 + - - +
620A LEU* 3.0 28.1 + - - +
645A TYR* 4.4 3.1 - - + -
759A ILE 4.5 0.3 - - - +
760A LEU* 3.6 24.9 - - + +
761A VAL* 3.6 7.4 + - - +
762A HIS* 2.5 41.5 + - - -
763A THR* 2.6 42.9 + - - +
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Residues in contact with ILE 617 (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 LEU* 3.9 14.6 - - + -
609A VAL* 4.8 2.5 - - + -
613A LYS* 3.0 55.9 - - + +
614A GLY 3.2 7.9 + - - +
615A ALA 3.1 0.6 - - - -
616A ASP* 1.3 75.9 - - - +
618A ALA* 1.3 66.7 + - - +
620A LEU* 3.3 2.0 + - - -
621A TRP* 3.1 19.9 + - - +
638A LEU* 4.7 9.2 - - + -
641A THR* 3.3 26.9 - - + +
642A SER* 4.2 16.4 - - - +
645A TYR* 4.5 22.7 - - + -
646A ARG* 5.7 4.0 - - - +
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Residues in contact with ALA 618 (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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65A MET* 4.9 10.8 - - + -
72A ILE* 4.2 14.4 - - + -
142A LEU* 4.8 10.3 - - + -
606A PRO* 6.4 0.4 - - + -
609A VAL* 3.6 27.3 - - + +
610A VAL* 5.0 1.8 - - + -
614A GLY 3.2 5.2 + - - +
615A ALA* 3.0 11.7 + - - +
617A ILE* 1.3 78.4 - - - +
619A ARG* 1.3 61.4 + - - +
621A TRP* 3.4 13.0 - - - +
622A VAL* 3.1 24.8 + - - +
638A LEU* 5.6 0.4 - - - -
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Residues in contact with ARG 619 (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 ILE* 3.9 29.8 - - + +
75A ASP* 2.4 37.7 + - - +
76A PHE* 3.6 23.0 - - + -
142A LEU 3.0 15.7 + - - +
143A GLY 3.1 24.4 + - - -
144A VAL* 3.5 5.5 - - - +
615A ALA 2.9 19.3 + - - +
616A ASP* 3.7 7.6 - - - +
618A ALA* 1.3 73.8 - - - +
620A LEU* 1.3 66.6 + - - +
621A TRP 3.1 1.6 - - - -
622A VAL* 3.0 13.2 + - - +
623A SER* 3.1 10.7 + - - -
758A PRO 3.1 25.7 + - - -
759A ILE* 2.8 24.7 - - - +
761A VAL* 3.6 19.1 - - - +
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Residues in contact with LEU 620 (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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616A ASP 3.0 17.5 + - - +
617A ILE* 3.3 0.4 + - - -
619A ARG* 1.3 76.3 - - - +
621A TRP* 1.3 62.0 + - - +
623A SER* 2.9 31.0 + - - +
624A SER* 3.2 11.1 + - - -
641A THR* 3.8 20.4 - - + +
644A ASP* 4.1 10.8 - - + -
645A TYR* 3.8 39.7 - - + +
648A ILE* 4.4 16.8 - - + -
705A TYR* 3.8 19.7 - - + -
756A LEU* 6.3 1.8 - - + -
759A ILE* 4.4 10.2 - - + +
760A LEU* 4.3 14.6 - - + -
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Residues in contact with TRP 621 (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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65A MET* 4.0 22.9 - - + -
69A LEU* 4.7 9.4 - - + -
588A VAL* 4.0 17.7 - - + -
617A ILE 3.1 12.4 + - - +
618A ALA* 3.4 16.4 - - - +
619A ARG 3.1 0.4 - - - -
620A LEU* 1.3 76.0 - - - +
622A VAL* 1.3 88.2 + - + +
624A SER* 2.5 28.9 + - - -
625A THR* 3.2 22.0 - - + +
631A VAL* 3.9 29.6 - - + -
632A ARG 3.2 22.6 + - - -
633A ILE* 3.6 28.8 - - + +
637A ILE* 3.7 22.7 - - + +
638A LEU* 4.1 16.8 - - + -
641A THR* 3.7 15.6 - - - +
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Residues in contact with VAL 622 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A LEU* 3.9 22.9 - - + -
72A ILE* 3.9 22.9 - - + -
73A LEU* 3.5 38.7 - - + +
76A PHE* 3.7 9.6 - - + -
618A ALA 3.1 14.5 + - - +
619A ARG 3.0 9.2 + - - +
621A TRP* 1.3 100.1 - - + +
623A SER* 1.3 63.8 + - - +
625A THR* 2.8 29.9 + - - +
627A TYR* 5.4 1.2 - - - -
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Residues in contact with SER 623 (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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76A PHE* 3.9 19.3 - - - -
619A ARG 3.1 9.5 + - - -
620A LEU* 2.9 29.4 + - - +
622A VAL* 1.3 76.6 - - - +
624A SER* 1.3 56.2 + - - +
625A THR 3.7 1.1 + - - +
701A TYR* 3.1 24.6 - - - +
702A LEU* 3.1 29.3 + - - +
705A TYR* 3.8 10.0 - - - +
759A ILE* 4.2 16.2 - - - +
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Residues in contact with SER 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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620A LEU 3.2 4.0 + - - -
621A TRP* 2.5 32.0 + - - -
623A SER* 1.3 78.5 - - - +
625A THR* 1.3 61.3 + - - +
641A THR* 5.0 2.3 + - - -
702A LEU* 3.2 12.0 - - - +
705A TYR* 3.5 46.7 + - - -
12T U 2.7 34.2 + - - +
13T C 3.7 0.2 - - - +
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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