Contacts of the helix formed by residues 90 - 104 (chain p) in PDB entry 6FF7
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 TYR 90 (chain p).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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452O PHE* 4.8 0.2 - - - +
453O LYS* 1.5 27.5 - - + +
49p VAL* 5.8 10.3 - - + +
53p VAL* 5.7 7.6 - - + +
83p PHE* 5.0 13.2 - - + -
88p ASP* 3.4 2.7 - - + +
89p PRO* 1.3 63.3 - - - +
91p HIS* 1.3 64.9 + - - +
92p ALA 3.2 3.1 - - - -
93p TYR* 2.9 26.1 + - + +
94p TYR* 3.1 12.4 + - - +
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Residues in contact with HIS 91 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449O GLN 3.1 23.0 + - - +
450O GLU* 4.5 0.9 - - - +
83p PHE 3.6 14.2 + - - +
84p LEU 5.5 0.4 - - - -
85p ASN 3.5 16.4 - - - +
86p PRO* 4.0 9.9 - - + +
88p ASP* 3.2 4.5 + - - +
89p PRO 3.2 1.4 - - - -
90p TYR* 1.3 77.1 - - - +
92p ALA* 1.3 62.4 + - - +
94p TYR* 3.2 13.8 + - - +
95p ARG* 3.3 12.0 + - - +
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Residues in contact with ALA 92 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89p PRO 4.3 8.1 + - - +
90p TYR 3.2 0.4 - - - -
91p HIS* 1.3 78.7 - - - +
93p TYR* 1.3 62.9 + - - +
95p ARG* 3.5 19.6 + - - +
96p HIS* 3.7 6.8 + - - +
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Residues in contact with TYR 93 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53p VAL* 5.9 3.1 - - + -
89p PRO 5.1 0.2 + - - -
90p TYR* 2.9 23.0 + - + +
92p ALA* 1.3 77.0 - - - +
94p TYR* 1.3 63.8 + - - +
96p HIS* 3.2 16.9 + - - +
97p LYS* 3.2 11.7 + - - +
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Residues in contact with TYR 94 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53p VAL* 4.6 24.5 - - + +
57p ALA* 4.2 4.3 - - + +
83p PHE* 5.3 8.3 - - + +
84p LEU* 6.3 1.1 - - - -
90p TYR 3.1 9.7 + - - +
91p HIS* 3.5 11.9 - - - +
93p TYR* 1.3 73.1 - - - +
95p ARG* 1.3 65.6 + - - +
97p LYS* 3.0 20.4 + - - +
98p VAL* 3.1 14.7 + - - +
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Residues in contact with ARG 95 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91p HIS 3.3 9.8 + - - +
92p ALA* 3.5 14.4 - - - +
93p TYR 3.3 0.4 - - - -
94p TYR* 1.3 77.6 - - - +
96p HIS* 1.3 63.2 + - - +
98p VAL* 3.6 11.8 + - - +
99p SER* 3.7 11.3 + - - -
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Residues in contact with HIS 96 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92p ALA 3.7 6.1 + - - +
93p TYR* 3.2 11.8 + - - +
94p TYR 3.2 0.4 - - - -
95p ARG* 1.3 77.8 - - - +
97p LYS* 1.3 65.0 + - - +
99p SER* 3.1 8.9 + - - -
100p GLU* 2.9 24.3 + - - +
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Residues in contact with LYS 97 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53p VAL* 4.9 0.7 - - + +
54p ASP* 4.6 13.7 - - - +
57p ALA* 3.4 22.2 - - + -
93p TYR 3.2 8.6 + - - +
94p TYR* 3.0 10.1 + - - +
96p HIS* 1.3 76.8 - - - +
98p VAL* 1.3 63.0 + - - +
100p GLU* 3.2 9.3 + - - +
101p PHE* 2.8 26.3 + - - +
106p ALA* 5.4 0.3 - - - +
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Residues in contact with VAL 98 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57p ALA* 3.7 22.6 - - + +
60p VAL* 5.6 4.9 - - + -
61p ALA* 3.3 15.4 - - + +
94p TYR 3.1 10.3 + - - +
95p ARG* 3.7 11.4 - - - +
96p HIS 3.2 0.4 + - - -
97p LYS* 1.3 76.3 - - - +
99p SER* 1.3 62.6 + - - +
102p LYS* 3.1 20.9 + - - +
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Residues in contact with SER 99 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95p ARG 3.7 7.3 + - - -
96p HIS* 3.1 10.4 + - - -
98p VAL* 1.3 78.1 - - - +
100p GLU* 1.3 56.4 + - - +
102p LYS* 3.3 8.6 + - - +
103p GLU* 3.0 28.3 + - - +
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Residues in contact with GLU 100 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96p HIS* 2.9 17.2 + - + +
97p LYS* 3.4 9.0 - - - +
99p SER* 1.3 73.4 - - - +
101p PHE* 1.3 64.7 + - - +
103p GLU* 3.2 8.0 + - - +
104p GLY 3.0 16.6 + - - -
105p LYS* 3.3 12.5 + - + -
106p ALA* 3.9 21.7 + - + +
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Residues in contact with PHE 101 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621M ARG* 4.8 7.8 - - - +
58p SER* 4.1 18.4 - - - +
61p ALA* 3.5 22.7 - - + -
97p LYS 2.8 16.8 + - - +
100p GLU* 1.3 72.9 - - - +
102p LYS* 1.3 62.8 + - - +
104p GLY* 3.0 15.5 + - - -
106p ALA* 4.5 3.9 - - + +
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Residues in contact with LYS 102 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61p ALA* 3.9 17.8 - - + +
98p VAL 3.1 13.9 + - - +
99p SER* 3.4 12.3 - - - +
100p GLU 3.2 0.2 - - - -
101p PHE* 1.3 78.1 - - - +
103p GLU* 1.3 60.0 + - - +
104p GLY* 3.3 1.2 + - - -
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Residues in contact with GLU 103 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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658M VAL* 4.7 14.6 - - - +
99p SER 3.0 13.8 + - - +
100p GLU* 3.2 12.3 + - - +
102p LYS* 1.3 75.7 - - - +
104p GLY* 1.3 61.4 + - - +
105p LYS* 4.5 11.0 - - + +
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Residues in contact with GLY 104 (chain p).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620M THR* 3.1 8.8 - - - +
621M ARG* 2.9 16.2 + - - -
100p GLU 3.0 1.2 + - - -
101p PHE 3.0 17.6 + - - -
102p LYS 3.1 2.1 - - - -
103p GLU* 1.3 78.3 - - - +
105p LYS* 1.3 57.9 + - - +
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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