Contacts of the helix formed by residues 558 - 571 (chain C) in PDB entry 1ES7
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 THR 558 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A LEU* 4.2 16.8 - - + +
105A ASP* 4.1 24.5 - - - +
557C SER* 1.3 76.2 - - - +
559C ASN* 1.3 64.9 + - - +
560C HIS* 3.7 7.3 + - - +
561C ALA* 3.1 22.8 + - - +
562C ILE* 3.1 24.2 + - - +
613C CYS 4.1 0.4 + - - -
614C ARG* 3.8 34.6 + - - +
781D GLU* 5.4 3.4 - - - -
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Residues in contact with ASN 559 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A TYR* 4.5 10.7 - - - +
104A GLN 2.9 34.8 + - - +
105A ASP* 4.1 2.8 + - - +
106A MET* 3.8 16.4 - - - -
558C THR* 1.3 73.4 - - - +
560C HIS* 1.3 63.4 + - - +
562C ILE* 3.0 9.4 + - - +
563C VAL* 2.9 27.3 + - - +
781D GLU* 3.2 29.7 + - - +
782D GLY* 3.3 31.7 + - - -
785D PHE* 4.1 9.6 - - + -
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Residues in contact with HIS 560 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 5.5 1.1 - - + -
38A TYR* 5.1 0.4 - - - -
40A ALA* 3.3 13.5 + - + +
41A PHE 2.7 28.8 + - - -
42A TYR* 4.3 1.6 - - - -
81A PRO* 4.5 7.8 - - + +
84A LEU* 3.9 10.8 - - + -
105A ASP 3.0 21.3 + - - +
106A MET* 3.2 26.7 - - - +
108A VAL* 3.1 29.7 - - + +
558C THR* 3.2 4.0 - - - +
559C ASN* 1.3 77.0 - - - +
561C ALA* 1.3 53.2 + - - +
563C VAL* 3.2 6.9 + - + +
564C GLN* 2.7 61.5 + - + +
614C ARG 4.9 2.0 + - - +
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Residues in contact with ALA 561 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551C LEU* 4.0 2.0 - - + -
557C SER* 3.9 6.5 - - - -
558C THR* 3.1 19.3 + - - +
560C HIS* 1.3 79.5 + - - +
562C ILE* 1.3 55.6 + - - +
564C GLN* 3.4 6.9 + - - +
565C THR* 2.8 37.7 + - - -
577C ALA* 4.1 10.4 - - + +
613C CYS 3.5 24.2 - - - +
614C ARG* 4.0 17.2 + - - +
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Residues in contact with ILE 562 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549C PHE* 5.9 0.6 - - + -
551C LEU* 3.4 25.1 - - + -
557C SER* 3.8 10.5 - - - +
558C THR 3.1 15.8 + - - +
559C ASN* 3.0 13.2 + - - +
561C ALA* 1.3 73.7 - - - +
563C VAL* 1.3 65.3 + - - +
565C THR* 3.0 15.5 + - - -
566C LEU* 3.0 16.0 + - + +
781D GLU 5.1 3.6 - - - +
782D GLY* 3.9 12.8 - - - +
785D PHE* 3.8 24.7 - - + -
786D GLN* 3.3 47.8 - - + +
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Residues in contact with VAL 563 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 6.3 0.7 - - + -
21A VAL* 4.3 19.3 - - + -
28A TRP* 4.7 13.5 - - + -
38A TYR* 3.9 24.5 - - + +
40A ALA* 5.4 2.7 - - + -
106A MET* 4.5 5.8 - - + -
559C ASN 2.9 20.6 + - - +
560C HIS* 3.7 5.6 - - + +
562C ILE* 1.3 74.2 - - - +
564C GLN* 1.3 65.0 + - - +
566C LEU* 3.1 10.5 + - - +
567C VAL* 3.0 33.0 + - + +
785D PHE* 4.1 32.5 - - + -
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Residues in contact with GLN 564 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 4.9 4.9 - - + -
42A TYR* 3.8 19.4 - - + +
43A CYS 5.0 4.9 + - - +
81A PRO* 5.6 1.7 - - - +
560C HIS* 2.7 47.9 + - + +
561C ALA* 3.7 5.8 - - - +
563C VAL* 1.3 74.8 - - - +
565C THR* 1.3 57.8 + - - +
567C VAL* 3.3 7.4 + - - +
568C ASN* 3.0 26.9 + - - +
574C ILE* 4.1 11.4 - - + +
575C PRO* 2.7 34.4 + - - +
576C LYS 3.4 19.7 + - - -
577C ALA* 4.0 6.1 - - - +
614C ARG 4.9 5.5 - - - +
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Residues in contact with THR 565 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547C CYS 4.4 6.5 + - - +
548C PRO 4.0 23.6 - - - +
549C PHE* 4.0 22.9 - - + -
551C LEU* 3.8 17.0 - - + +
561C ALA 2.8 19.9 + - - -
562C ILE* 3.0 9.2 + - - -
564C GLN* 1.3 77.6 - - - +
566C LEU* 1.3 61.5 + - - +
568C ASN* 3.4 10.6 + - + +
569C SER* 3.3 19.6 + - - -
576C LYS* 5.3 7.9 - - + +
577C ALA* 4.1 18.6 + - - +
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Residues in contact with LEU 566 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A VAL* 6.1 1.8 - - + -
28A TRP* 3.4 35.2 - - + -
549C PHE* 3.7 23.3 - - + -
562C ILE* 3.0 17.9 + - + +
563C VAL* 3.1 8.0 + - - +
565C THR* 1.3 73.0 - - - +
567C VAL* 1.3 66.7 + - + +
569C SER* 2.9 20.8 + - - -
570C VAL* 3.2 13.2 + - - +
785D PHE* 3.6 26.7 - - + +
786D GLN 4.6 0.4 - - - +
789D ASP* 3.3 28.0 - - - +
790D SER* 3.9 17.3 - - - +
797D ARG* 3.7 6.5 - - - +
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Residues in contact with VAL 567 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 4.5 12.3 - - + -
21A VAL* 4.3 17.3 - - + -
26A VAL* 4.6 17.5 - - + -
563C VAL* 3.0 29.8 + - + +
564C GLN* 3.5 10.3 - - - +
566C LEU* 1.3 75.6 - - + +
568C ASN* 1.3 57.7 + - - +
570C VAL* 2.9 12.4 + - + +
571C ASN* 2.8 28.6 + - + +
574C ILE* 3.6 31.2 - - + -
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Residues in contact with ASN 568 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564C GLN 3.0 13.4 + - - +
565C THR* 3.6 13.4 - - - +
566C LEU 3.2 0.2 - - - -
567C VAL* 1.3 77.4 - - - +
569C SER* 1.3 63.4 + - - +
571C ASN 3.4 21.0 - - - -
572C SER* 3.5 20.9 + - - +
574C ILE* 2.7 28.6 + - - +
575C PRO* 4.0 8.5 - - - +
576C LYS* 3.5 40.3 + - + +
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Residues in contact with SER 569 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549C PHE* 4.6 5.4 - - - +
565C THR 3.3 11.7 + - - -
566C LEU* 2.9 15.3 + - - -
568C ASN* 1.3 79.3 + - - +
570C VAL* 1.3 54.6 + - - +
790D SER* 6.1 0.2 - - - -
793D ALA* 4.0 6.1 - - - -
794D GLN* 2.7 37.5 + - - +
795D LEU 4.8 0.3 + - - -
797D ARG* 2.9 41.8 + - - -
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Residues in contact with VAL 570 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ASP* 4.5 11.0 - - + +
26A VAL* 4.6 15.7 - - + -
566C LEU 3.5 14.4 - - - +
567C VAL* 2.9 9.0 + - + +
569C SER* 1.3 81.6 - - - +
571C ASN* 1.3 62.4 + - + +
572C SER 4.4 0.2 - - - -
790D SER* 3.4 29.2 - - - +
792D LYS* 3.4 29.5 - - + +
793D ALA 4.3 0.4 - - - +
794D GLN* 3.9 19.8 + - - +
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Residues in contact with ASN 571 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567C VAL* 2.8 17.7 + - + +
568C ASN* 3.4 7.5 - - - +
569C SER 3.5 0.4 - - - -
570C VAL* 1.3 86.0 + - + +
572C SER* 1.3 60.0 + - - +
573C LYS* 2.8 51.0 + - - +
574C ILE* 3.3 16.7 + - + +
794D GLN* 5.3 1.8 - - - -
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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