Contacts of the helix formed by residues 86 - 102 (chain F) in PDB entry 2NVT
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 THR 86 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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852A TYR* 4.4 6.9 + - + -
1059A HIS* 3.2 23.8 - - + +
1060A PRO* 3.8 37.4 + - + +
82F THR* 5.4 5.6 - - + +
84F TYR 4.9 2.0 - - - +
85F MET* 1.3 75.2 - - - +
87F LYS* 1.3 68.7 + - - +
88F TYR* 3.5 8.2 + - - +
89F GLU* 2.8 52.1 + - - +
90F ARG* 3.0 12.3 + - - +
136F ARG* 4.9 3.1 - - - +
155F LEU* 4.2 1.1 - - - -
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Residues in contact with LYS 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A LYS* 6.4 0.4 - - - +
503A GLN 5.4 5.8 + - - +
504A LEU* 3.7 29.3 + - + +
509A LEU* 4.9 8.7 + - - +
510A GLN* 6.0 0.6 - - - +
874A ASP* 6.2 0.2 - - - +
1059A HIS* 2.9 33.7 + - + +
1062A GLU* 4.4 7.5 + - - +
1141B HIS 5.3 0.8 + - - -
86F THR* 1.3 73.2 - - - +
88F TYR* 1.3 105.6 + - + +
90F ARG* 3.2 4.8 + - - +
91F ALA* 2.9 26.3 + - - +
155F LEU* 3.5 20.5 - - + +
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Residues in contact with TYR 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A LEU* 4.1 10.1 - - + -
1059A HIS* 4.0 6.5 - - + -
1060A PRO 3.9 18.2 - - - +
1061A GLY 4.7 0.2 - - - -
1062A GLU* 2.9 61.1 + - + +
1063A MET 4.4 1.7 + - - -
1437A GLY* 3.6 19.3 - - - +
1438A THR* 3.6 22.0 - - - +
1441A PHE* 3.0 17.8 - - + -
1140B ALA 4.6 3.8 + - - -
1141B HIS 3.4 25.1 + - - -
1142B GLY* 3.8 12.6 - - - -
86F THR* 3.2 4.8 - - - +
87F LYS* 1.3 102.3 - - + +
89F GLU* 1.3 62.1 + - - +
91F ALA* 4.2 5.7 - - - +
92F ARG* 3.6 10.2 + - - +
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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
----------------------------------------------------------
852A TYR* 3.2 12.9 + - - +
1441A PHE* 3.4 22.7 - - + -
85F MET* 3.8 13.2 - - + -
86F THR* 2.8 48.0 + - - +
88F TYR* 1.3 72.1 - - - +
90F ARG* 1.3 64.6 + - - +
92F ARG* 3.0 14.0 + - - +
93F ILE* 3.0 18.4 + - - +
134F ILE* 3.3 30.3 - - + +
136F ARG* 2.7 41.6 + - - -
151F LEU* 4.8 0.8 - - - +
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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
----------------------------------------------------------
503A GLN* 2.9 30.5 + - + +
85F MET* 3.6 29.6 - - + +
86F THR 3.0 8.7 + - - +
87F LYS* 3.6 9.2 - - - +
89F GLU* 1.3 73.9 - - - +
91F ALA* 1.3 72.3 + - - +
93F ILE* 2.7 14.4 + - + -
94F LEU* 2.8 41.4 + - + +
122F MET* 3.5 26.1 - - - +
125F LEU* 4.0 21.9 - - + +
153F VAL* 4.5 5.5 - - + +
155F LEU* 3.5 32.4 - - - +
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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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496A GLU* 5.2 0.9 - - - +
499A ALA* 4.2 9.0 - - - +
500A GLU* 4.9 8.7 + - - +
503A GLN* 4.4 20.2 - - + +
504A LEU* 3.8 32.5 - - + -
1438A THR* 4.6 3.8 - - - +
87F LYS 2.9 20.6 + - - +
88F TYR 4.2 4.5 - - - +
90F ARG* 1.3 76.9 - - + +
92F ARG* 1.3 60.4 + - - +
94F LEU* 4.1 4.0 - - - +
95F GLY* 3.3 17.0 + - - -
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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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496A GLU* 5.8 6.6 - - + +
500A GLU* 5.8 1.1 - - - -
1433A MET* 4.3 26.5 - - - +
1438A THR* 3.3 32.4 + - + +
1439A GLY* 5.5 1.4 - - - -
1441A PHE* 3.6 23.8 + - + -
1442A ASP* 4.2 12.9 + - - +
1443A VAL* 3.9 32.4 - - + +
1145B SER* 4.7 6.6 + - - +
88F TYR 3.6 5.5 + - - +
89F GLU 3.0 8.8 + - - +
90F ARG 2.9 0.6 + - - -
91F ALA* 1.3 75.7 - - - +
93F ILE* 1.3 59.6 + - - +
95F GLY* 3.5 1.4 + - - -
96F THR* 2.8 49.4 + - - +
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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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1441A PHE* 5.0 0.4 - - + -
1443A VAL* 4.2 13.2 - - + -
85F MET* 3.7 23.1 - - + -
89F GLU* 3.0 24.3 + - - +
90F ARG 2.7 11.8 + - - +
92F ARG* 1.3 72.4 - - + +
94F LEU* 1.3 70.1 + - - +
96F THR* 3.0 4.8 + - - -
97F ARG* 2.8 22.1 + - - +
125F LEU* 4.3 8.5 - - + -
130F ILE* 4.0 28.9 - - + -
132F LEU* 4.5 11.8 - - + +
134F ILE* 3.3 30.7 - - + -
148F VAL* 3.7 18.2 - - + -
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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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499A ALA* 4.9 2.5 - - + -
503A GLN* 4.3 14.4 - - + +
90F ARG* 2.8 61.4 + - + +
91F ALA 4.1 2.9 - - - +
93F ILE* 1.3 75.8 - - + +
95F GLY* 1.3 52.9 + - - +
97F ARG* 3.0 2.8 + - - +
98F ALA* 2.5 39.5 + - - +
118F LEU* 4.8 10.3 - - + -
121F ALA* 3.6 15.1 - - + +
122F MET* 3.6 41.3 - - + +
125F LEU* 4.0 15.0 - - + -
130F ILE* 5.2 0.4 - - + -
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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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496A GLU* 3.1 36.6 + - - +
499A ALA* 3.9 9.8 - - - +
91F ALA 3.3 8.8 + - - -
92F ARG 3.7 1.6 - - - -
93F ILE 3.2 1.2 - - - -
94F LEU* 1.3 78.0 - - - +
96F THR* 1.3 51.5 + - - +
98F ALA* 3.1 6.1 + - - +
99F LEU* 2.7 35.2 + - - +
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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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496A GLU* 4.0 6.3 - - - +
1443A VAL* 4.6 13.1 - - + +
92F ARG* 2.8 41.8 + - - +
93F ILE* 3.0 4.6 + - - -
95F GLY* 1.3 71.2 - - - -
97F ARG* 1.3 61.0 + - - +
99F LEU* 3.4 9.1 - - + +
100F GLN* 3.0 33.9 + - + +
132F LEU* 4.5 16.6 - - + -
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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 2.8 15.1 + - - +
94F LEU* 3.3 8.5 - - - +
96F THR* 1.3 68.7 - - - +
98F ALA* 1.3 52.2 + - - +
99F LEU 2.8 5.3 + - - -
100F GLN* 2.8 65.3 + - - +
101F ILE* 2.8 43.9 + - + +
105F ALA* 5.2 1.0 + - - +
106F PRO 3.3 24.5 + - - -
107F VAL* 4.4 0.6 - - - +
108F PHE* 3.7 18.2 - - - -
121F ALA* 3.8 10.8 - - + -
124F GLU* 3.0 44.7 + - - +
130F ILE* 4.0 33.4 - - + +
131F PRO* 4.5 8.6 - - - +
132F LEU* 5.0 1.7 - - + +
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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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495A GLU* 3.3 19.8 - - + +
94F LEU 2.5 23.7 + - - +
95F GLY* 3.3 8.5 - - - +
97F ARG* 1.3 70.7 - - - +
99F LEU* 1.3 56.7 + - - +
101F ILE* 4.0 2.5 - - - -
102F SER* 3.0 26.2 + - - -
117F PRO* 3.5 13.8 - - - +
118F LEU* 3.9 31.9 - - + +
121F ALA* 4.1 1.5 - - + +
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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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494A SER* 4.2 8.3 - - - +
495A GLU* 3.9 19.5 - - + +
496A GLU* 4.0 18.2 - - - +
95F GLY 2.7 11.2 + - - +
96F THR* 3.4 15.3 - - + +
97F ARG 2.8 1.4 + - - -
98F ALA* 1.3 77.3 - - - +
100F GLN* 1.3 68.4 + - + +
101F ILE 3.1 1.3 - - - -
102F SER* 2.9 19.0 + - - +
103F MET* 3.4 32.9 + - - +
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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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1445A ILE* 6.0 2.4 - - - +
96F THR* 3.0 28.3 - - + +
97F ARG* 2.8 44.9 + - - +
99F LEU* 1.3 78.3 - - + +
101F ILE* 1.3 62.2 + - - +
103F MET* 3.4 7.8 + - - +
104F ASN 3.6 0.2 + - - -
105F ALA* 3.2 40.0 + - + +
131F PRO* 5.7 5.7 - - - +
132F LEU* 4.6 14.7 - - - +
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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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381A THR* 4.5 1.0 - - - +
383A TYR* 4.3 20.4 - - + -
97F ARG* 2.8 46.5 + - + +
100F GLN* 1.3 74.2 - - - +
102F SER* 1.3 58.4 + - - +
103F MET 2.8 10.8 + - - -
104F ASN* 3.3 12.0 + - - -
105F ALA 4.5 6.4 - - - +
106F PRO 5.5 0.7 - - - +
107F VAL* 4.7 9.4 - - + -
117F PRO* 3.8 36.6 - - + +
120F ILE* 3.8 26.7 - - + -
121F ALA* 3.8 3.8 - - - +
124F GLU* 3.1 26.2 - - - +
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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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376A TYR* 5.6 0.4 - - - -
379A VAL* 3.5 24.0 - - - +
381A THR* 3.2 20.1 + - - -
383A TYR* 6.2 0.7 - - - -
495A GLU* 3.5 15.6 - - - +
98F ALA 3.0 16.8 + - - -
99F LEU* 2.9 22.3 + - - +
101F ILE* 1.3 77.8 - - - +
103F MET* 1.3 58.6 + - - +
104F ASN 3.7 0.4 - - - -
117F PRO* 3.7 23.3 - - - +
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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
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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