Contacts of the helix formed by residues 590 - 607 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189H ARG* 3.7 6.3 - - - -
588H ARG 3.6 2.1 + - - -
589H ILE* 1.3 75.3 - - - +
591H GLN* 1.3 67.6 + - - -
592H GLN 3.3 2.5 - - - -
593H THR* 2.9 10.1 + - - -
594H VAL* 2.8 26.4 + - - +
7I C 3.1 21.5 + - - -
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Residues in contact with GLN 591 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189H ARG* 2.9 40.8 + - - +
191H PHE* 5.1 9.0 - - + -
211H LEU 4.6 4.2 - - - +
212H LYS* 5.4 5.4 - - + +
213H SER* 3.1 33.9 + - - +
215H ASP* 3.4 23.1 + - - +
216H PHE* 4.6 5.5 - - - -
590H GLY* 1.3 70.3 - - - +
592H GLN* 1.3 66.2 + - + +
594H VAL* 3.1 8.7 + - - +
595H ASP* 3.0 23.1 + - - +
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Residues in contact with GLN 592 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152H THR* 3.2 27.7 - - + +
156H LYS* 4.4 13.2 + - - +
212H LYS* 4.0 23.8 - - - +
590H GLY 3.3 0.4 - - - -
591H GLN* 1.3 82.7 - - + +
593H THR* 1.3 55.9 + - - +
595H ASP* 3.4 2.6 + - - +
596H SER* 2.7 39.0 + - - +
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Residues in contact with THR 593 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109G PHE* 3.7 32.1 - - + -
148H SER* 3.9 6.8 + - - +
151H VAL* 4.7 2.9 - - + -
152H THR* 4.1 14.5 + - - +
581H ILE* 5.0 0.2 - - - -
589H ILE* 4.0 7.9 - - + -
590H GLY* 2.9 12.5 + - - -
592H GLN* 1.3 76.2 - - - +
594H VAL* 1.3 61.1 + - - +
596H SER* 3.8 4.6 - - - -
597H LEU* 2.8 33.0 + - + +
7I C 2.9 30.2 + - - +
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Residues in contact with VAL 594 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191H PHE* 5.2 9.0 - - + -
211H LEU* 4.3 11.0 - - + +
578H ALA* 4.7 6.5 - - + +
581H ILE* 3.4 27.6 - - + -
582H ILE* 4.4 12.3 - - + -
589H ILE* 3.5 24.2 - - + +
590H GLY 2.8 24.7 + - - +
591H GLN* 3.5 7.6 - - - +
593H THR* 1.3 71.2 - - - +
595H ASP* 1.3 60.0 + - - +
597H LEU* 2.8 2.8 + - - +
598H LEU* 2.6 53.9 + - + +
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Residues in contact with ASP 595 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159H LYS* 2.8 32.8 + - - -
210H GLY* 3.3 9.6 - - - -
211H LEU* 2.9 42.3 + - - +
212H LYS* 3.6 27.5 + - + +
591H GLN 3.0 9.6 + - - +
592H GLN 3.5 9.2 - - - +
594H VAL* 1.3 78.6 - - - +
596H SER* 1.3 54.0 + - - +
598H LEU* 3.2 5.2 + - - +
599H PHE* 2.7 38.5 + - - +
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Residues in contact with SER 596 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151H VAL* 3.7 22.7 - - - -
152H THR* 3.7 12.3 - - - +
155H ALA* 3.3 28.6 - - - +
159H LYS* 5.8 0.2 - - - -
592H GLN* 2.7 22.8 + - - +
593H THR* 3.8 2.5 - - - -
595H ASP* 1.3 76.6 + - - +
597H LEU* 1.3 58.1 + - - +
599H PHE* 4.3 2.7 - - - -
600H LEU* 2.6 44.1 + - - +
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Residues in contact with LEU 597 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102G VAL* 4.4 8.1 - - + +
103G VAL* 3.7 35.4 - - + +
106G CYS* 5.2 3.1 - - + -
109G PHE* 4.0 17.9 - - + -
151H VAL* 3.4 28.0 - - + -
581H ILE* 3.4 35.4 - - + -
586H ARG* 4.4 18.4 - - - +
589H ILE* 4.9 1.3 - - + -
593H THR 2.8 23.7 + - - +
594H VAL 2.8 5.7 + - - +
596H SER* 1.3 70.2 - - - +
598H LEU* 1.3 61.9 + - - +
600H LEU* 4.1 1.0 - - - +
601H ASN* 3.1 24.9 + - - +
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Residues in contact with LEU 598 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208H ILE* 4.5 21.1 - - + +
210H GLY* 6.2 0.7 - - - -
211H LEU* 3.2 44.9 - - + -
574H THR* 4.5 11.4 - - + +
577H LEU* 3.9 35.2 - - + +
578H ALA* 3.9 13.5 - - + +
581H ILE* 4.9 8.3 - - + -
594H VAL* 2.6 32.1 + - + +
595H ASP* 3.6 2.9 - - - +
597H LEU* 1.3 70.8 - - - +
599H PHE* 1.3 65.1 + - - +
601H ASN* 3.2 8.6 + - - +
602H SER* 3.1 18.5 + - - -
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Residues in contact with PHE 599 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155H ALA 4.8 0.4 - - - -
158H LYS* 4.5 5.2 - - + -
159H LYS* 3.3 52.5 - - + -
162H ILE* 4.3 13.0 - - + -
207H LEU* 6.1 2.2 - - + -
208H ILE* 3.9 20.1 - - - +
209H LEU* 3.4 22.4 - - + +
210H GLY* 5.7 0.9 - - - -
235H PHE* 3.6 22.9 - + - -
595H ASP* 2.7 25.5 + - - +
596H SER* 3.6 4.3 - - - +
598H LEU* 1.3 71.4 - - - +
600H LEU* 1.3 81.4 + - + +
602H SER* 2.9 14.3 + - - -
603H PHE* 2.9 36.0 + + + -
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Residues in contact with LEU 600 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G VAL* 4.4 16.2 - - + -
151H VAL* 3.9 10.3 - - + +
154H ASP* 4.1 23.8 - - + +
155H ALA* 3.3 37.5 - - + +
158H LYS* 4.3 12.3 - - + -
596H SER* 2.6 33.1 + - - +
597H LEU 4.1 2.7 - - - +
599H PHE* 1.3 83.5 - - + +
601H ASN* 1.3 64.9 + - - +
602H SER 3.1 0.2 + - - -
603H PHE* 3.1 9.1 + - + +
604H TYR* 2.9 51.9 + - + +
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Residues in contact with ASN 601 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G VAL* 3.6 27.8 + - - +
104G ARG* 3.9 18.8 + - - +
106G CYS* 6.4 0.7 - - - -
577H LEU* 4.8 11.1 - - + +
597H LEU 3.1 19.5 + - - +
598H LEU* 3.4 5.8 - - - +
599H PHE 3.1 0.2 - - - -
600H LEU* 1.3 77.1 - - - +
602H SER* 1.3 62.9 + - - +
604H TYR* 3.4 14.7 + - - +
605H LYS* 3.5 34.3 + - - +
3K A 5.7 0.5 - - - +
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Residues in contact with SER 602 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206H ASP 3.5 0.7 + - - -
207H LEU* 3.4 4.0 - - - +
208H ILE* 3.0 54.8 + - - +
598H LEU 3.1 6.8 + - - -
599H PHE 2.9 10.7 + - - -
601H ASN* 1.3 73.1 - - - +
603H PHE* 1.3 68.6 + - - +
605H LYS* 2.8 22.4 + - - +
606H ASN* 3.1 32.2 + - - +
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Residues in contact with PHE 603 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158H LYS* 3.6 66.2 - - + -
161H LEU* 4.5 20.0 - - + -
162H ILE* 4.8 1.8 - - + -
207H LEU* 5.0 3.7 - - - +
599H PHE* 2.9 28.3 + + + +
600H LEU* 3.4 10.3 - - - +
602H SER* 1.3 75.7 - - - +
604H TYR* 1.3 69.5 + + + +
606H ASN* 5.0 1.6 - - - +
607H PHE* 2.8 72.6 + + + +
608H CYS* 4.0 15.7 - - - -
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Residues in contact with TYR 604 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100G GLN* 3.9 36.4 + - + +
103G VAL* 4.2 13.6 - - + +
104G ARG* 4.2 26.0 - - + +
154H ASP* 3.4 21.7 + - - -
158H LYS* 4.0 18.4 - - - -
600H LEU* 2.9 51.9 + - + +
601H ASN* 3.7 10.8 - - - +
602H SER 3.2 0.8 - - - -
603H PHE* 1.3 88.6 - + - +
605H LYS* 1.3 62.5 + - + +
608H CYS* 3.5 36.4 + - + +
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Residues in contact with LYS 605 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208H ILE* 5.1 9.8 - - - +
577H LEU* 4.6 11.3 - - - +
601H ASN* 3.5 40.3 + - - +
602H SER* 2.8 15.9 + - - +
604H TYR* 1.3 75.4 - - + +
606H ASN* 1.3 65.5 + - - +
607H PHE 3.7 0.2 + - - -
608H CYS 4.1 9.2 - - - +
2K G 4.4 0.8 + - - -
3K A 2.8 45.4 + - - +
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Residues in contact with ASN 606 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203H GLU* 5.1 2.1 - - - +
204H LEU 4.8 1.6 - - - +
205H ARG* 3.5 29.9 + - - +
206H ASP* 2.8 46.3 + - - +
207H LEU* 3.0 31.6 - - + +
602H SER* 3.1 26.3 + - - +
603H PHE 4.2 0.7 - - - +
605H LYS* 1.3 85.4 - - - +
607H PHE* 1.3 68.3 + - + +
608H CYS 3.8 1.3 + - - -
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Residues in contact with PHE 607 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162H ILE* 3.2 50.5 - - + -
165H GLU* 4.1 8.5 - - + -
166H ILE* 5.6 0.9 - - + -
198H TYR* 3.5 18.6 - - - -
205H ARG* 3.6 32.1 - - - -
207H LEU* 4.4 18.8 - - + -
603H PHE* 2.8 51.6 + + + +
606H ASN* 1.3 86.3 - - + +
608H CYS* 1.3 73.1 + - - +
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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