Contacts of the helix formed by residues 590 - 608 (chain G) in PDB entry 4D1Q
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 590 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189G ARG* 4.1 2.7 - - - -
588G ARG 3.6 3.4 + - - -
589G ILE* 1.3 70.6 - - - +
591G GLN* 1.3 63.6 + - - -
592G GLN* 2.9 5.2 - - - -
593G THR* 2.5 30.1 + - - -
594G VAL* 3.0 9.2 + - - +
7K C 2.6 24.4 + - - -
8K A 6.0 1.3 - - - -
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Residues in contact with GLN 591 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189G ARG* 3.4 26.7 - - - +
191G PHE* 4.1 18.8 - - + -
211G LEU 4.6 6.0 - - - +
212G LYS* 5.9 1.8 - - + -
213G SER* 3.6 26.9 + - - +
215G ASP* 4.7 6.6 - - - +
590G GLY* 1.3 73.1 - - - -
592G GLN* 1.3 89.6 + - - +
594G VAL* 3.0 21.2 + - - +
595G ASP* 3.1 14.3 + - - +
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Residues in contact with GLN 592 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152G THR* 4.3 12.9 - - + +
156G LYS* 5.3 6.8 + - - -
212G LYS* 5.8 6.9 - - - +
590G GLY* 2.8 5.0 + - - +
591G GLN* 1.3 96.5 + - - +
593G THR* 1.3 66.0 + - - +
595G ASP* 3.1 15.4 + - - +
596G SER* 3.1 17.4 + - - -
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Residues in contact with THR 593 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148G SER* 3.8 9.8 + - - +
151G VAL* 5.1 2.2 - - + -
152G THR* 3.7 21.5 - - + +
589G ILE* 4.0 12.3 - - + -
590G GLY* 2.5 15.5 + - - -
592G GLN* 1.3 72.6 - - - +
594G VAL* 1.3 57.5 + - - -
596G SER* 4.4 1.1 - - - -
597G LEU* 2.8 35.2 + - + +
109H PHE* 3.5 37.9 - - + -
7K C 3.2 18.5 + - - +
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Residues in contact with VAL 594 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189G ARG* 5.0 0.9 - - - +
191G PHE* 5.3 6.1 - - + -
211G LEU* 4.9 7.6 - - + +
578G ALA* 4.5 8.7 - - + -
581G ILE* 4.3 19.5 - - + -
582G ILE* 4.3 19.1 - - + -
589G ILE* 4.0 26.0 - - + +
590G GLY 3.0 20.1 + - - +
591G GLN* 3.0 9.1 + - - +
593G THR* 1.3 75.1 - - - +
595G ASP* 1.3 69.0 + - - +
597G LEU* 4.2 4.3 - - - -
598G LEU* 3.0 37.0 + - + +
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Residues in contact with ASP 595 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159G LYS* 3.2 32.9 + - - +
209G LEU 4.5 0.2 - - - +
210G GLY* 3.4 10.4 - - - -
211G LEU* 2.9 43.3 + - - +
212G LYS* 3.8 16.7 - - + +
234G GLN* 4.0 7.3 + - - +
591G GLN 3.1 10.6 + - - +
592G GLN* 3.2 13.0 - - - +
594G VAL* 1.3 72.0 - - - +
596G SER* 1.3 71.6 + - - +
598G LEU* 2.8 7.1 + - - +
599G PHE* 2.8 22.3 + - - +
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Residues in contact with SER 596 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151G VAL* 3.0 32.7 + - - -
152G THR* 3.6 14.3 + - - +
155G ALA* 3.2 25.5 - - - +
159G LYS* 5.1 1.2 + - - -
592G GLN 3.1 13.9 + - - -
593G THR 3.8 2.5 - - - -
595G ASP* 1.3 80.8 + - - +
597G LEU* 1.3 67.5 + - - -
598G LEU 2.8 0.5 + - - -
599G PHE* 2.8 10.4 + - - -
600G LEU* 2.9 17.6 + - - +
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Residues in contact with LEU 597 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151G VAL* 3.4 26.2 - - + +
581G ILE* 3.8 38.3 - - + +
586G ARG* 4.7 10.3 - - - +
593G THR* 2.8 24.8 + - + +
594G VAL* 4.0 2.7 - - - +
596G SER* 1.3 73.0 - - - +
598G LEU* 1.3 60.4 + - - +
600G LEU* 4.5 0.9 - - - +
601G ASN* 3.4 21.4 + - + +
102H VAL* 4.5 11.2 - - + +
103H VAL* 4.3 30.7 - - + +
106H CYS* 5.0 6.5 - - - -
107H ARG 5.1 0.2 - - - +
109H PHE* 3.7 25.6 - - + -
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Residues in contact with LEU 598 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208G ILE* 4.3 17.8 - - + +
211G LEU* 3.5 39.3 - - + +
574G THR* 4.1 11.0 - - + +
577G LEU* 3.6 40.5 - - + +
578G ALA* 3.9 12.1 - - + +
581G ILE* 3.8 19.7 - - + -
594G VAL* 3.0 21.3 + - + +
595G ASP* 2.8 6.5 + - - +
596G SER 2.8 3.0 + - - -
597G LEU* 1.3 72.1 - - - +
599G PHE* 1.3 59.1 + - - +
601G ASN* 3.6 7.4 + - + +
602G SER* 3.2 23.7 + - - -
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Residues in contact with PHE 599 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155G ALA* 4.2 2.0 - - + -
158G LYS* 3.9 13.5 - - + -
159G LYS* 3.2 63.9 - - + -
162G ILE* 4.7 3.6 - - + -
207G LEU* 4.8 14.6 - - + -
208G ILE* 3.3 28.7 - - + +
209G LEU 4.5 5.8 - - - +
210G GLY* 5.7 0.9 - - - -
235G PHE* 4.1 13.2 - + - -
595G ASP* 2.8 23.8 + - - +
596G SER* 2.8 2.6 + - - +
598G LEU* 1.3 69.2 - - - +
600G LEU* 1.3 80.0 + - + +
601G ASN 3.0 1.1 - - - -
602G SER* 2.9 4.3 + - - +
603G PHE* 2.8 46.5 + + + +
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Residues in contact with LEU 600 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151G VAL* 3.8 15.5 - - + +
154G ASP* 3.7 29.4 - - + +
155G ALA* 3.2 38.6 - - + +
158G LYS* 4.2 10.3 - - + -
596G SER 2.9 21.8 + - - +
597G LEU 4.5 0.9 - - - +
599G PHE* 1.3 80.0 - - + +
601G ASN* 1.3 63.1 + - - +
603G PHE* 3.4 2.9 + - - -
604G TYR* 3.1 55.3 + - + +
103H VAL* 4.3 20.2 - - + -
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Residues in contact with ASN 601 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577G LEU* 4.5 12.0 - - - +
597G LEU 3.4 19.9 + - - +
598G LEU* 3.7 7.7 - - + +
599G PHE 3.0 0.8 - - - -
600G LEU* 1.3 80.4 - - - +
602G SER* 1.3 61.5 + - - +
604G TYR* 3.6 5.3 + - - +
605G LYS* 3.0 53.5 + - - +
103H VAL* 3.1 30.6 + - - +
104H ARG* 3.5 19.2 + - - +
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Residues in contact with SER 602 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206G ASP 3.6 7.6 + - - -
207G LEU* 3.5 14.0 - - - +
208G ILE* 3.2 47.7 + - - +
598G LEU 3.2 8.0 + - - -
599G PHE* 2.9 8.5 + - - -
601G ASN* 1.3 75.0 + - - +
603G PHE* 1.3 68.6 + - - +
605G LYS* 2.8 22.3 + - - +
606G ASN* 2.9 15.8 + - - +
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Residues in contact with PHE 603 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158G LYS* 3.4 51.6 - - + -
161G LEU* 4.7 7.9 - - + -
162G ILE* 4.1 12.6 - - + -
207G LEU* 4.8 7.1 - - - +
599G PHE* 2.8 38.4 + + + +
600G LEU* 3.6 6.1 - - - +
602G SER* 1.3 71.6 - - - +
604G TYR* 1.3 81.3 + + - +
607G PHE* 2.6 74.7 + + + +
608G CYS* 4.3 11.9 - - - -
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Residues in contact with TYR 604 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154G ASP* 3.6 19.6 + - - -
158G LYS* 4.3 9.4 + - - -
600G LEU* 3.1 32.2 + - + +
601G ASN* 3.9 5.6 - - - +
603G PHE* 1.3 100.4 - + - +
605G LYS* 1.3 62.4 + - + +
608G CYS* 3.4 35.1 + - + +
100H GLN* 3.7 36.1 + - + +
103H VAL* 3.9 21.9 - - + +
104H ARG* 3.6 34.5 - - + +
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Residues in contact with LYS 605 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577G LEU* 4.4 12.7 - - - +
601G ASN* 3.0 45.3 + - - +
602G SER* 2.8 17.3 + - - +
604G TYR* 1.3 75.9 - - + +
606G ASN* 1.3 64.1 + - - +
607G PHE 3.8 0.2 + - - -
608G CYS 3.9 9.4 - - - +
609G LYS* 5.1 2.8 + - - +
3I A 2.9 53.6 + - - +
4I G 6.1 0.4 - - - -
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Residues in contact with ASN 606 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204G LEU 4.1 3.5 - - - +
205G ARG* 3.1 33.6 + - - -
206G ASP* 2.7 51.7 + - - +
207G LEU* 3.3 29.5 - - + +
602G SER* 2.9 13.1 + - - +
603G PHE 4.2 0.2 - - - +
605G LYS* 1.3 83.4 - - - +
607G PHE* 1.3 74.5 + - + +
608G CYS 3.7 0.6 + - - -
609G LYS* 4.3 7.1 + - - -
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Residues in contact with PHE 607 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162G ILE* 3.0 52.5 - - + -
165G GLU* 4.6 7.4 - - + -
198G TYR* 3.4 25.8 - - - -
205G ARG* 3.6 24.5 - - - -
207G LEU* 4.4 12.1 - - + -
603G PHE* 2.6 53.1 + + + +
606G ASN* 1.3 103.1 - - + +
608G CYS* 1.3 68.8 + - - +
609G LYS* 4.9 2.9 - - - -
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Residues in contact with CYS 608 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603G PHE* 4.3 20.2 - - - -
604G TYR* 3.4 29.3 + - + +
605G LYS 3.9 6.9 - - - +
606G ASN 3.7 0.8 + - - -
607G PHE* 1.3 90.0 - - - +
609G LYS* 1.3 82.4 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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