Contacts of the helix formed by residues 588 - 595 (chain A) in PDB entry 6Q6Q
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 588 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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586A HIS* 3.1 12.8 + - - -
587A LEU* 1.3 76.6 - - - +
589A GLY* 1.3 52.0 + - - +
590A VAL 3.6 1.6 - - - -
591A LYS* 3.2 24.0 + - - +
592A HIS* 2.7 61.6 + - - -
802A ARG* 3.2 24.4 + - - -
1046A GLU* 6.0 0.5 - - - +
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Residues in contact with GLY 589 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A ALA* 3.6 15.2 - - - +
112A THR* 3.8 19.6 + - - +
585A MET* 4.7 4.7 - - - -
586A HIS* 2.8 22.1 + - - -
587A LEU 3.1 1.0 - - - -
588A SER* 1.3 76.2 - - - +
590A VAL* 1.3 62.5 + - - +
592A HIS* 3.0 17.0 + - - +
593A ALA* 3.1 8.8 + - - +
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Residues in contact with VAL 590 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A THR* 4.3 18.6 - - + -
99A ILE* 4.6 17.3 - - + -
103A GLN 5.0 2.9 - - - +
104A GLU* 5.3 7.0 - - - -
107A ALA* 3.8 18.6 - - + +
108A LYS* 5.4 6.5 - - + -
585A MET* 4.2 21.4 - - + +
587A LEU 4.7 7.2 + - - +
589A GLY* 1.3 73.2 - - - +
591A LYS* 1.3 64.6 + - + +
593A ALA* 3.0 3.6 + - + -
594A THR* 2.9 35.0 + - - +
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Residues in contact with LYS 591 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A THR* 5.1 8.5 - - + -
587A LEU* 3.4 23.6 + - - +
588A SER* 3.2 26.9 + - - +
589A GLY 3.1 0.4 - - - -
590A VAL* 1.3 83.1 - - + +
592A HIS* 1.3 63.7 + - - +
594A THR* 3.8 5.8 - - - -
595A GLY 3.3 3.5 + - - -
596A GLU* 3.2 23.6 + - + +
597A ALA* 3.1 36.1 + - + +
801A ARG* 5.9 2.0 - - - +
802A ARG* 4.0 12.6 - - - +
1071A HIS* 6.3 1.0 - - - -
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Residues in contact with HIS 592 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A THR* 3.9 15.0 - - + -
113A GLN 3.6 15.1 + - - -
114A CYS 3.2 18.4 - - - -
115A GLY* 3.5 20.0 - - - -
118A THR* 3.3 20.5 - - - +
119A PRO* 3.7 13.2 - - - +
586A HIS* 3.7 9.8 - + - -
588A SER* 2.7 48.6 + - - -
589A GLY* 3.0 11.9 + - - +
591A LYS* 1.3 73.3 - - - +
593A ALA* 1.3 61.0 + - - +
594A THR 3.6 0.2 + - - -
595A GLY* 3.8 4.9 + - - -
597A ALA* 3.7 7.4 - - + +
599A TYR* 3.0 20.0 + + - -
802A ARG* 4.2 11.7 - - - -
1046A GLU* 6.4 0.7 - - + -
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Residues in contact with ALA 593 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A VAL* 3.2 17.7 - - - +
103A GLN* 3.2 48.8 - - + +
106A ILE* 4.1 11.7 - - + -
107A ALA* 4.1 3.8 - - + -
118A THR* 3.6 9.6 - - + -
122A VAL* 3.7 5.8 - - - +
589A GLY 3.1 10.1 + - - +
590A VAL* 3.0 9.7 + - - +
592A HIS* 1.3 79.0 - - - +
594A THR* 1.3 57.8 + - - +
595A GLY 3.5 0.4 - - - -
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Residues in contact with THR 594 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A VAL* 3.6 11.9 - - - +
90A GLU* 4.1 18.0 + - - +
93A GLY 4.0 5.5 - - - +
94A SER* 4.1 3.8 - - - -
95A THR* 4.6 0.4 - - + +
99A ILE* 3.6 24.0 - - + -
103A GLN* 3.4 35.2 - - + +
590A VAL* 2.9 18.7 + - - +
591A LYS* 3.7 2.1 + - - -
593A ALA* 1.3 75.7 - - - +
595A GLY* 1.3 60.8 + - - +
596A GLU* 2.7 41.0 + - - +
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Residues in contact with GLY 595 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A THR* 4.4 6.4 + - - -
39A GLY* 3.7 34.0 + - - -
41A LYS* 3.9 9.2 + - - -
89A VAL* 3.8 5.8 - - - +
90A GLU* 5.0 3.0 - - - +
119A PRO* 4.5 2.9 - - - -
591A LYS 3.3 5.8 + - - -
592A HIS* 3.8 6.2 + - - -
593A ALA 3.5 3.0 - - - -
594A THR* 1.3 76.1 - - - +
596A GLU* 1.3 61.9 + - - +
597A ALA* 3.2 9.7 + - - +
598A ILE* 5.6 0.2 - - - +
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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