Contacts of the helix formed by residues 568 - 582 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B THR* 3.4 15.0 - - - +
179B ILE 4.7 3.4 + - - -
180B ASP* 4.7 4.9 - - - -
246B VAL* 4.3 0.7 + - - +
247B THR* 3.5 10.9 - - - -
248B ASP* 3.3 26.2 + - - +
265B CYS* 3.4 14.6 - - - +
268B HIS* 4.3 5.2 - - - -
567B SER* 1.3 73.2 - - - +
569B ALA* 1.3 65.4 + - - +
570B ALA 3.2 1.6 - - - -
571B SER* 3.0 18.6 + - - -
572B GLU* 3.2 26.6 + - - +
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Residues in contact with ALA 569 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B CYS* 5.0 0.8 - - - -
319B TRP* 5.0 4.1 - - + -
375B GLN* 3.8 26.2 - - + +
377B CYS* 5.6 1.8 - - - -
567B SER* 3.0 19.1 + - - +
568B SER* 1.3 77.0 - - - +
570B ALA* 1.3 52.0 + - - +
572B GLU* 3.1 11.9 + - - +
573B ARG* 2.8 60.6 + - - +
16F G 4.2 4.5 + - - +
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Residues in contact with ALA 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B THR* 3.9 4.5 - - + +
195B THR* 3.6 26.8 - - + +
197B HIS* 3.7 20.0 - - + -
206B ASP* 4.2 3.6 - - - +
377B CYS* 4.1 7.1 - - - -
565B PRO* 6.1 0.4 - - + -
567B SER 4.3 3.1 + - - +
568B SER 3.1 1.2 + - - -
569B ALA* 1.3 76.2 - - - +
571B SER* 1.3 64.1 + - - +
573B ARG* 3.0 25.6 + - - +
574B THR* 2.9 23.5 + - - -
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Residues in contact with SER 571 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B THR* 3.0 27.9 + - - -
179B ILE* 3.1 14.3 + - - -
180B ASP* 4.0 23.8 - - - -
193B GLY 4.1 6.7 + - - -
195B THR* 3.2 6.5 + - - -
568B SER* 3.0 10.5 + - - -
570B ALA* 1.3 77.3 - - - +
572B GLU* 1.3 65.9 + - - +
574B THR* 2.9 28.1 + - - -
575B PHE* 3.2 14.0 + - - -
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Residues in contact with GLU 572 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B ASP* 2.9 25.7 - - - +
268B HIS* 3.2 23.5 + - - -
319B TRP* 4.7 4.3 - - + -
568B SER* 3.2 15.6 + - - +
569B ALA* 3.1 10.5 + - - +
571B SER* 1.3 74.3 - - - +
573B ARG* 1.3 65.2 + - - +
575B PHE* 2.9 27.5 + - - +
576B SER 3.0 9.2 + - - -
15F T 3.4 20.2 + - + +
16F G 3.2 56.4 + - - +
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Residues in contact with ARG 573 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ASP* 4.3 6.3 + - - -
375B GLN 2.5 31.3 + - - -
377B CYS* 4.2 11.1 - - - -
569B ALA* 2.8 32.4 + - - +
570B ALA* 3.2 37.7 - - - +
572B GLU* 1.3 73.6 - - - +
574B THR* 1.3 62.1 + - - +
576B SER* 2.9 15.2 + - - -
577B LEU* 3.0 21.9 + - + +
1E A 2.9 33.4 + - + -
2E G 3.1 59.2 + - - +
3E A 5.8 0.9 - - - +
15F T 3.5 5.8 + - - -
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Residues in contact with THR 574 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B GLY* 5.1 7.5 - - - -
194B VAL 5.7 2.0 + - - +
195B THR* 4.3 5.0 + - - +
208B ILE* 3.9 37.5 - - + +
210B GLY 5.2 0.2 - - - +
211B LEU* 4.4 18.2 - - + -
570B ALA 2.9 18.6 + - - -
571B SER* 2.9 15.1 + - - -
573B ARG* 1.3 74.4 - - - +
575B PHE* 1.3 69.9 + - + +
577B LEU* 2.9 16.7 + - - +
578B ALA* 2.8 25.3 + - - +
598B LEU* 4.6 6.2 - - + +
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Residues in contact with PHE 575 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B ASP* 3.2 43.7 - - + -
181B LEU 3.7 9.6 - - - -
182B TRP* 3.2 61.6 - + + +
193B GLY* 4.0 23.3 - - - -
211B LEU* 4.3 9.9 - - + -
571B SER* 3.5 17.3 - - - -
572B GLU* 3.2 20.0 - - - +
574B THR* 1.3 82.1 - - + +
576B SER* 1.3 57.5 + - - +
578B ALA* 3.2 7.9 + - - +
579B GLY* 2.8 27.4 + - - -
15F T 4.3 9.8 - - - +
16F G 4.8 1.3 - - - -
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Residues in contact with SER 576 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572B GLU 3.0 4.9 + - - -
573B ARG 2.9 14.8 + - - -
575B PHE* 1.3 76.7 - - - +
577B LEU* 1.3 60.7 + - - +
579B GLY* 3.3 9.5 + - - -
580B ASN* 3.2 20.1 + - - +
2E G 3.8 7.0 + - - -
3E A 5.2 1.9 + - - -
14F C 2.5 40.2 + - - -
15F T 3.3 28.6 + - - -
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Residues in contact with LEU 577 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ILE* 4.2 22.4 - - + -
573B ARG* 3.0 21.1 + - + +
574B THR* 2.9 8.0 + - - +
576B SER* 1.3 73.5 - - - +
578B ALA* 1.3 58.2 + - - +
579B GLY 2.9 1.6 - - - -
580B ASN* 2.6 43.4 + - - +
581B ILE* 3.4 8.5 + - - +
598B LEU* 4.1 14.8 - - + -
601B ASN* 5.0 10.8 - - - +
605B LYS* 4.6 14.8 - - - +
3E A 4.5 33.4 - - + +
4E G 6.1 0.2 - - - -
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Residues in contact with ALA 578 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B TRP* 3.8 16.8 - - + -
211B LEU* 3.8 30.1 - - + -
574B THR 2.8 11.9 + - - +
575B PHE* 3.4 11.4 - - - +
577B LEU* 1.3 74.2 - - - +
579B GLY* 1.3 64.1 + - - +
581B ILE* 3.0 7.6 + - - +
582B ILE* 2.9 26.7 + - + +
594B VAL* 4.8 3.8 - - + -
598B LEU* 4.0 14.5 - - + +
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Residues in contact with GLY 579 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585A LYS* 5.7 0.4 - - - -
182B TRP* 4.3 12.5 - - - -
575B PHE 2.8 13.1 + - - -
576B SER* 3.5 8.1 - - - -
577B LEU 2.9 0.6 - - - -
578B ALA* 1.3 79.7 - - - +
580B ASN* 1.3 61.0 + - - +
581B ILE 3.3 0.5 + - - -
582B ILE* 3.6 18.4 + - - +
583B THR* 4.0 2.8 + - - -
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Residues in contact with ASN 580 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A CYS* 3.9 21.2 - - - -
585A LYS* 3.1 45.1 + - - +
576B SER* 3.2 12.9 + - - +
577B LEU* 2.6 53.5 + - - +
579B GLY* 1.3 70.9 - - - -
581B ILE* 1.3 59.3 + - - -
583B THR* 3.3 15.6 + - - -
586B ARG* 4.3 4.5 + - - -
3E A 5.7 2.6 - - - +
4E G 5.4 10.0 - - - +
14F C 5.9 1.7 + - - -
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Residues in contact with ILE 581 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A CYS* 4.1 15.3 - - - -
577B LEU 3.6 9.4 - - - +
578B ALA* 3.0 7.1 + - - +
580B ASN* 1.3 79.1 - - - +
582B ILE* 1.3 60.1 + - + +
583B THR 2.8 12.2 + - - -
586B ARG* 3.3 36.3 - - - +
589B ILE* 3.6 28.1 - - + +
594B VAL* 4.1 15.0 - - + +
597B LEU* 3.9 27.8 - - + +
598B LEU* 3.3 36.6 - - + -
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Residues in contact with ILE 582 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B TRP* 4.5 10.3 - - + -
184B ASP* 4.0 28.0 - - + +
185B ASN* 5.1 3.9 - - - +
186B TYR* 3.4 28.4 - - + -
187B ILE* 6.0 1.3 - - + -
189B ARG* 3.6 26.9 - - - +
191B PHE* 4.3 10.5 - - + -
578B ALA 2.9 12.9 + - - +
579B GLY* 3.6 10.2 - - - +
581B ILE* 1.3 72.5 - - - +
583B THR* 1.3 61.3 + - - +
586B ARG 4.6 0.4 - - - -
587B ASN* 5.0 5.2 - - - -
588B ARG 5.9 0.4 - - - +
589B ILE* 4.0 11.9 - - + -
594B VAL* 3.8 32.3 - - + -
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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