Contacts of the helix formed by residues 88 - 103 (chain F) in PDB entry 6CNC
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 88 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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534A LEU* 3.9 11.2 - - + -
1085A PRO 4.2 7.6 - - - -
1086A GLY* 3.5 12.1 - - - -
1087A THR* 2.6 58.5 + - - +
1088A ALA 4.6 0.3 + - - -
1424A GLY* 4.3 11.9 - - - -
1425A THR* 4.3 19.5 - - - +
1428A PHE* 3.7 25.1 - + + -
1073B TYR 3.4 25.1 + - - -
1074B GLY* 4.6 5.2 - - - -
86F THR* 2.8 14.7 + - + -
87F LYS* 1.3 101.8 + - - +
89F GLU* 1.3 67.5 + - - +
91F ALA* 2.9 3.5 + - - -
92F ARG* 2.9 23.6 + - - +
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Residues in contact with GLU 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1428A PHE* 3.9 9.1 - - - -
85F MET* 2.9 53.4 - - + +
86F THR* 3.2 32.2 - - + +
88F TYR* 1.3 74.1 - - - +
90F ARG* 1.3 90.2 + - - +
93F ILE* 2.9 35.1 + - + +
125F LEU* 3.9 14.9 - - - +
134F ILE* 3.5 25.6 - - + -
136F ARG* 5.0 1.3 - - - +
148F VAL* 4.7 6.4 - - - +
151F LEU* 3.9 10.2 - - + +
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Residues in contact with ARG 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533A ASN* 2.6 51.5 + - - +
539A ASN* 5.8 2.7 - - - +
85F MET* 4.0 22.6 - - + +
87F LYS* 3.9 20.9 - - - +
88F TYR 3.3 0.4 - - - -
89F GLU* 1.3 94.0 + - - +
91F ALA* 1.3 57.8 + - - +
94F LEU* 3.4 22.8 - - + +
122F MET* 4.7 14.1 - - - -
125F LEU* 4.4 14.9 - - + +
153F VAL* 4.2 19.8 + - - +
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Residues in contact with ALA 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529A ALA 4.2 8.4 - - - +
530A GLU* 3.7 19.5 - - - +
533A ASN* 4.0 7.0 - - - +
534A LEU* 4.4 20.2 - - + -
1425A THR* 4.1 8.3 - - - +
87F LYS 3.5 6.1 + - - +
88F TYR* 2.9 22.5 + - - +
90F ARG* 1.3 80.7 - - - +
92F ARG* 1.3 66.7 + - - +
94F LEU* 3.8 1.4 - - - +
95F GLY* 2.9 19.4 + - - -
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Residues in contact with ARG 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526A GLU* 5.3 4.4 + - - +
530A GLU* 4.8 2.2 - - - -
1420A THR* 6.0 1.0 - - - -
1425A THR* 3.1 48.6 + - + +
1426A GLY* 3.4 17.0 - - - -
1428A PHE* 3.8 25.0 + - + -
1429A LYS* 6.0 0.4 - - - +
1430A VAL* 3.7 32.9 - - + +
1076B SER* 3.7 6.5 + - - -
1077B GLN* 3.8 16.9 - - + +
88F TYR 2.9 12.9 + - - +
91F ALA* 1.3 74.7 - - - +
93F ILE* 1.3 58.3 + - - +
95F GLY* 4.2 2.2 - - - +
96F THR* 2.8 41.6 + - - +
61G PRO* 3.8 33.1 + - - +
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Residues in contact with ILE 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1428A PHE* 5.3 2.7 - - + -
1430A VAL* 3.8 22.7 - - + -
89F GLU* 2.9 28.6 + - - +
92F ARG* 1.3 76.1 - - - +
94F LEU* 1.3 63.7 + - + +
96F THR* 4.3 1.3 - - - -
97F ARG* 2.9 28.3 + - + +
125F LEU* 3.8 24.2 - - + -
130F ILE* 3.9 22.2 - - + -
132F LEU* 4.3 11.2 - - + +
134F ILE* 3.6 39.0 - - + -
148F VAL* 4.3 12.1 - - + -
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Residues in contact with LEU 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529A ALA* 4.1 8.1 - - + +
533A ASN* 3.3 22.2 - - + +
90F ARG* 3.4 26.6 + - + +
91F ALA 3.4 2.3 + - - +
92F ARG 3.4 0.2 - - - -
93F ILE* 1.3 79.8 - - + +
95F GLY* 1.3 63.9 + - - +
97F ARG* 4.0 4.2 - - - +
98F ALA* 2.9 26.0 + - - +
118F LEU* 5.1 7.7 - - + +
121F ALA* 4.3 6.4 - - + +
122F MET* 3.5 50.7 - - + +
125F LEU* 3.6 37.5 - - + -
130F ILE* 5.1 0.9 - - + -
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Residues in contact with GLY 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526A GLU* 3.7 25.2 - - - +
529A ALA* 3.6 19.7 - - - +
530A GLU* 6.1 0.2 - - - -
91F ALA 2.9 15.0 + - - -
92F ARG* 3.1 4.0 + - - -
94F LEU* 1.3 78.2 - - - +
96F THR* 1.3 65.0 + - - +
98F ALA* 3.4 2.9 - - - +
99F LEU 2.9 18.7 + - - -
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Residues in contact with THR 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526A GLU* 4.0 10.9 + - - -
1430A VAL* 4.3 7.7 - - - +
92F ARG* 2.8 36.4 + - - +
93F ILE* 4.3 1.1 - - - -
95F GLY* 1.3 69.8 - - - -
97F ARG* 1.3 62.8 + - - +
99F LEU* 3.1 9.7 + - + +
100F GLN* 2.9 32.6 + - + +
132F LEU* 4.6 9.2 - - + -
59G LEU* 3.4 35.6 - - + +
61G PRO* 5.4 3.8 + - - +
64G GLY* 5.1 6.7 - - - -
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Residues in contact with ARG 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93F ILE 2.9 19.9 + - - +
94F LEU* 4.0 3.1 - - - +
96F THR* 1.3 77.1 - - - +
98F ALA* 1.3 64.1 + - - +
100F GLN* 3.2 28.3 + - - +
101F ILE* 3.0 42.3 + - + +
105F ALA* 5.1 4.4 - - - +
106F PRO 3.2 24.7 + - - -
107F VAL* 4.3 3.8 - - - +
108F PHE* 4.5 6.9 - - - +
121F ALA* 4.1 13.5 - - + -
124F GLU* 3.2 35.4 + - - +
130F ILE* 4.0 33.1 - - + +
131F PRO* 4.4 17.8 - - - +
132F LEU* 4.7 7.9 - - + +
18G PHE* 5.5 4.2 - - - -
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Residues in contact with ALA 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525A GLU* 4.6 10.5 - - - +
94F LEU 2.9 20.3 + - - +
95F GLY* 3.4 5.2 - - - +
97F ARG* 1.3 76.9 - - - +
99F LEU* 1.3 64.2 + - - +
101F ILE* 2.8 18.4 + - - +
102F SER 2.9 9.7 + - - -
117F PRO* 3.6 10.5 - - + +
118F LEU* 3.8 34.3 - - + +
121F ALA* 4.1 8.7 - - + +
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Residues in contact with LEU 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407A LYS* 5.6 2.2 - - - +
524A THR* 4.0 20.0 - - - +
525A GLU* 4.2 15.4 - - + +
526A GLU* 4.4 24.0 - - + +
95F GLY 2.9 13.3 + - - +
96F THR* 3.1 11.2 + - + +
98F ALA* 1.3 74.0 - - - +
100F GLN* 1.3 63.9 + - - +
102F SER* 2.3 32.9 + - - +
103F MET* 3.4 23.2 + - + +
61G PRO 5.3 1.6 - - - +
62G GLY 5.0 4.9 - - - +
63G ASP 3.0 31.9 - - - +
64G GLY* 4.2 8.5 - - - -
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Residues in contact with GLN 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1432A LYS* 4.9 7.7 - - - +
96F THR* 2.9 23.1 + - + +
97F ARG* 3.2 37.7 + - - +
99F LEU* 1.3 77.2 - - - +
101F ILE* 1.3 63.9 + - - +
103F MET* 2.8 18.8 + - - +
104F ASN 3.8 0.2 + - - -
105F ALA* 3.7 19.5 - - + +
132F LEU* 4.5 11.0 - - - +
15G PRO* 4.3 11.4 - - + +
18G PHE* 4.0 21.9 - - - -
59G LEU* 3.9 20.2 - - - +
64G GLY* 3.7 25.2 + - - +
66G SER* 5.2 0.2 - - - -
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Residues in contact with ILE 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409A THR* 3.8 9.6 + - + +
411A TYR* 4.4 15.4 - - + -
97F ARG* 3.0 54.6 + - + +
98F ALA* 2.8 13.7 + - - +
100F GLN* 1.3 72.3 - - - +
102F SER* 1.3 61.4 + - - +
103F MET 3.2 0.9 + - - -
104F ASN* 3.3 11.4 + - - -
105F ALA* 4.3 8.4 + - + +
106F PRO 4.1 4.5 - - - +
107F VAL* 3.7 22.2 - - + -
117F PRO* 4.3 13.2 - - + +
120F ILE* 3.5 33.9 - - + -
121F ALA* 5.1 0.9 - - + -
124F GLU* 4.7 0.2 - - - +
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Residues in contact with SER 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406A GLU* 5.7 1.8 - - - -
407A LYS* 3.5 29.3 + - - +
409A THR* 3.3 24.0 - - - +
525A GLU* 3.9 26.0 - - - +
98F ALA 2.9 9.2 + - - -
99F LEU* 2.3 32.4 + - - +
101F ILE* 1.3 78.3 - - - +
103F MET* 1.3 59.6 + - - +
104F ASN 3.3 1.6 - - - -
117F PRO* 4.1 13.9 - - - +
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Residues in contact with MET 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407A LYS* 3.6 31.6 - - + +
409A THR* 4.1 0.7 - - - -
458A ILE 5.6 2.2 - - - +
99F LEU* 3.8 19.1 - - + +
100F GLN 2.8 11.5 + - - +
102F SER* 1.3 79.5 + - - +
104F ASN* 1.3 68.0 + - - +
105F ALA 3.8 0.2 - - - -
12G ARG* 5.6 1.3 - - - +
15G PRO* 3.6 35.6 - - + +
16G ASP* 3.0 17.5 - - - +
63G ASP* 3.8 34.1 - - - +
64G GLY 5.2 0.2 - - - -
65G SER* 4.7 7.6 - - - +
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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