Contacts of the helix formed by residues 568 - 580 (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 SER 568 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178G THR* 3.2 23.1 - - - +
179G ILE 4.5 5.8 - - - -
180G ASP* 4.4 5.8 + - - -
246G VAL* 3.8 11.7 - - - +
247G THR* 4.3 7.2 - - - -
248G ASP* 4.0 5.4 + - - +
265G CYS* 3.3 25.8 - - - +
268G HIS* 3.9 15.4 + - - -
567G SER* 1.3 70.5 - - - +
569G ALA* 1.3 52.9 + - - +
570G ALA 3.0 3.4 - - - -
571G SER* 2.8 26.2 + - - -
572G GLU* 3.2 11.8 + - - +
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Residues in contact with ALA 569 (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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265G CYS* 4.8 1.6 - - - -
319G TRP* 4.8 5.3 - - + -
375G GLN* 3.8 35.2 - - + +
377G CYS* 6.3 0.2 - - - -
567G SER* 3.0 20.0 + - - +
568G SER* 1.3 76.0 + - - +
570G ALA* 1.3 61.7 + - - +
572G GLU* 3.1 14.2 + - - +
573G ARG* 3.0 33.3 + - - +
16J G 4.2 9.1 + - - +
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Residues in contact with ALA 570 (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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178G THR* 3.8 7.6 - - - +
195G THR* 3.4 32.7 - - + +
197G HIS* 3.7 20.0 - - + +
206G ASP* 4.5 4.0 - - - +
208G ILE* 5.8 0.3 - - - +
377G CYS* 4.3 4.2 - - - -
567G SER 4.0 2.5 + - - +
568G SER 3.0 0.4 - - - -
569G ALA* 1.3 78.4 - - - +
571G SER* 1.3 59.9 + - - +
573G ARG* 3.4 22.3 + - - +
574G THR* 3.0 21.5 + - - -
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Residues in contact with SER 571 (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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178G THR* 3.1 38.2 + - - +
179G ILE* 3.7 1.0 + - - -
180G ASP* 3.9 20.9 - - - -
193G GLY 3.6 17.2 + - - -
195G THR* 3.9 3.6 - - - +
568G SER 2.8 5.3 + - - -
570G ALA* 1.3 76.9 - - - +
572G GLU* 1.3 66.4 + - - -
574G THR* 2.7 24.3 + - - -
575G PHE* 3.1 19.3 + - - -
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Residues in contact with GLU 572 (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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180G ASP* 3.0 30.4 - - - +
268G HIS* 3.2 29.6 + - - -
319G TRP* 4.2 3.6 - - + -
568G SER* 3.2 10.2 + - - -
569G ALA* 3.1 12.1 + - - +
571G SER* 1.3 75.8 - - - +
573G ARG* 1.3 57.8 + - - +
575G PHE* 3.1 34.3 + - - +
576G SER 3.2 5.0 + - - -
15J T 3.2 14.6 + - + +
16J G 3.2 59.5 - - - +
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Residues in contact with ARG 573 (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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206G ASP* 4.7 2.8 + - - -
375G GLN* 3.3 27.9 + - - +
377G CYS* 3.9 18.4 - - - +
569G ALA* 3.0 16.7 + - - +
570G ALA* 3.4 31.4 + - - +
572G GLU* 1.3 72.8 - - - +
574G THR* 1.3 65.2 + - - +
575G PHE 2.9 2.2 - - - -
576G SER* 3.2 3.9 + - - -
577G LEU* 2.9 31.2 + - + +
1I A 3.0 33.9 + - + -
2I G 3.0 60.2 + - - +
3I A 5.8 0.2 - - - -
15J T 3.8 13.2 - - - +
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Residues in contact with THR 574 (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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193G GLY* 5.2 3.8 - - - -
194G VAL 5.4 1.2 + - - +
195G THR* 3.3 18.6 - - + +
208G ILE* 3.7 43.7 - - + +
210G GLY 4.9 8.1 - - - +
211G LEU* 4.5 9.8 - - + +
570G ALA 3.0 17.1 + - - -
571G SER* 2.7 16.4 + - - -
573G ARG* 1.3 71.4 - - - +
575G PHE* 1.3 63.2 + - + +
577G LEU* 3.5 4.9 + - - +
578G ALA* 3.1 25.5 + - - +
598G LEU* 4.1 11.8 - - + +
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Residues in contact with PHE 575 (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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180G ASP* 3.4 48.2 - - + -
181G LEU 4.0 4.0 - - - -
182G TRP* 3.6 57.4 - + + -
192G LEU 5.0 0.2 - - - -
193G GLY* 4.0 9.9 - - - -
211G LEU* 3.7 29.2 - - + -
571G SER* 3.4 16.8 - - - -
572G GLU* 3.1 20.9 - - - +
574G THR* 1.3 78.1 - - - +
576G SER* 1.3 68.0 + - - +
577G LEU 3.0 1.1 - - - -
578G ALA* 2.7 19.1 + - - +
579G GLY* 2.8 10.2 + - - -
15J T 4.0 10.8 - - - -
16J G 4.7 1.1 - - - -
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Residues in contact with SER 576 (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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572G GLU 3.2 3.2 + - - -
573G ARG* 3.6 8.5 - - - -
575G PHE* 1.3 78.4 - - - +
577G LEU* 1.3 61.1 + - - +
579G GLY* 3.3 9.5 + - - +
580G ASN* 3.0 28.6 + - - +
2I G 3.6 11.8 + - - -
3I A 4.9 3.8 + - - -
14J C 2.8 32.5 + - - +
15J T 3.3 31.0 + - - -
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Residues in contact with LEU 577 (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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208G ILE* 4.1 25.6 - - + -
573G ARG* 2.9 21.4 + - + +
574G THR* 3.6 5.6 - - - +
575G PHE 2.8 0.8 + - - -
576G SER* 1.3 75.7 - - - +
578G ALA* 1.3 63.6 + - - +
579G GLY 3.1 0.9 - - - -
580G ASN* 3.1 25.4 + - - +
581G ILE* 3.6 12.1 - - - +
598G LEU* 3.6 15.7 - - + +
601G ASN* 4.5 10.3 - - - +
605G LYS* 4.4 17.0 - - - +
106H CYS* 5.0 1.0 - - - -
3I A 3.9 39.5 - - + +
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Residues in contact with ALA 578 (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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182G TRP* 4.1 16.6 - - + -
211G LEU* 3.5 32.8 - - + -
574G THR 3.1 7.5 + - - +
575G PHE 2.7 12.0 + - - +
577G LEU* 1.3 69.5 - - - +
579G GLY* 1.3 60.4 + - - +
581G ILE* 2.8 12.1 + - - +
582G ILE* 2.8 31.0 + - + +
594G VAL* 4.5 6.7 - - + -
598G LEU* 3.9 11.6 - - + +
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Residues in contact with GLY 579 (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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182G TRP* 4.4 14.9 - - - -
575G PHE 2.8 12.2 + - - -
576G SER* 3.5 7.4 - - - -
577G LEU 3.1 0.6 - - - -
578G ALA* 1.3 77.9 - - - +
580G ASN* 1.3 61.2 - - - +
581G ILE 3.4 0.5 + - - -
582G ILE* 3.4 21.5 - - - +
583G THR* 4.1 4.3 - - - +
584H GLU* 5.7 1.7 - - - +
15J T 6.5 0.7 - - - -
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Residues in contact with ASN 580 (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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576G SER* 3.0 24.9 + - - +
577G LEU* 3.1 24.8 + - - +
578G ALA 3.0 1.0 - - - -
579G GLY* 1.3 79.0 - - - +
581G ILE* 1.3 59.1 + - - +
583G THR* 3.2 18.7 - - - +
586G ARG* 4.4 3.6 + - - -
106H CYS* 3.9 20.2 - - - +
584H GLU* 5.5 2.4 - - - +
585H LYS* 3.2 42.5 + - - +
3I A 4.8 7.5 + - - +
4I G 4.5 11.5 + - - -
14J C 5.7 4.7 + - - +
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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