Contacts of the helix formed by residues 97 - 108 (chain C) in PDB entry 1V8C
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 PRO 97 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95C ALA* 3.4 9.6 - - - +
96C PHE* 1.3 90.3 - - - +
98C PRO* 1.3 77.3 - - + +
99C TRP* 3.2 42.4 - - + +
100C LEU* 3.0 26.8 + - + +
101C LEU* 3.1 11.4 + - - +
141C PRO* 5.8 10.7 - - + -
143C LEU* 4.2 0.2 - - - -
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Residues in contact with PRO 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C PHE 3.9 0.4 - - - +
97C PRO* 1.3 86.5 - - + +
99C TRP* 1.3 57.8 + - + +
101C LEU* 3.3 1.8 + - + +
102C GLU* 2.8 41.3 + - - +
127C PHE* 4.1 19.1 - - + -
129C GLU* 3.4 41.7 - - + +
141C PRO* 6.4 0.9 - - + -
143C LEU* 3.7 24.4 - - + -
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Residues in contact with TRP 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C PRO* 3.2 38.9 - - + +
98C PRO* 1.3 79.1 - - + +
100C LEU* 1.3 85.0 + - + +
102C GLU* 3.6 15.1 + - - +
103C ARG* 3.1 59.5 + - - +
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Residues in contact with LEU 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C ALA 5.3 1.8 - - - +
96C PHE* 4.1 20.6 - - + -
97C PRO* 3.0 29.0 + - + +
99C TRP* 1.3 105.3 - - + +
101C LEU* 1.3 66.0 + - - +
103C ARG* 3.1 15.5 + - + +
104C TYR* 3.1 48.5 + - + +
162C ALA 5.7 1.6 - - - +
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Residues in contact with LEU 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C PHE* 3.8 32.0 - - + -
97C PRO 3.1 10.3 + - - +
98C PRO* 3.8 6.1 - - + +
100C LEU* 1.3 77.4 - - - +
102C GLU* 1.3 58.8 + - + +
104C TYR* 3.2 8.8 + - + +
105C LEU* 2.8 53.0 + - + +
108C TRP* 5.3 0.7 - - + -
125C VAL* 4.8 1.1 - - + -
127C PHE* 3.7 34.3 - - + -
143C LEU* 3.8 15.7 - - + -
145C VAL* 3.9 19.3 - - + -
159C ILE* 4.1 20.9 - - + -
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Residues in contact with GLU 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C PRO* 2.8 30.7 + - - +
99C TRP* 3.6 14.6 - - - +
101C LEU* 1.3 77.4 - - - +
103C ARG* 1.3 56.6 + - - +
105C LEU* 3.2 8.2 + - - +
106C GLU* 2.8 41.7 + - - +
112C ARG* 5.2 5.7 + - - -
116C GLY 5.2 2.9 + - - -
118C TYR* 3.8 23.2 + - + +
127C PHE* 3.6 31.0 - - + -
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Residues in contact with ARG 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A GLU* 4.6 1.8 - - - +
99C TRP* 3.1 46.2 + - - +
100C LEU* 3.1 18.3 + - + +
102C GLU* 1.3 75.3 - - - +
104C TYR* 1.3 59.4 + - + +
106C GLU* 3.4 12.5 + - - +
107C GLU* 3.0 30.5 + - + +
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Residues in contact with TYR 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A SER* 3.6 29.4 - - - -
96C PHE* 4.5 4.9 - + - -
100C LEU* 3.1 50.4 + - + +
101C LEU* 3.5 9.4 - - + +
103C ARG* 1.3 76.0 - - + +
105C LEU* 1.3 65.6 + - - +
107C GLU* 3.1 11.7 + - - +
108C TRP* 3.0 53.1 + + + -
161C PHE* 5.6 2.9 - + - -
162C ALA* 3.7 39.0 + - + -
165C ARG* 4.0 15.2 + - - +
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Residues in contact with LEU 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C LEU* 2.8 39.4 + - + +
102C GLU* 3.2 4.5 + - - +
104C TYR* 1.3 71.9 - - - +
106C GLU* 1.3 55.2 - - - +
108C TRP* 3.3 24.4 + - + +
109C GLY 3.5 0.2 + - - -
110C GLY* 2.8 34.2 + - - -
118C TYR* 3.6 45.3 - - + -
120C LEU* 3.8 28.9 - - + +
125C VAL* 4.2 16.2 - - + -
127C PHE* 3.9 16.4 - - + -
159C ILE* 4.5 2.0 - - + -
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Residues in contact with GLU 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A GLU* 3.4 37.3 - - - +
102C GLU* 2.8 27.0 + - - +
103C ARG* 3.6 11.5 - - - +
105C LEU* 1.3 74.3 - - - +
107C GLU* 1.3 65.6 + - - +
109C GLY* 3.1 12.3 + - - -
110C GLY 4.3 10.4 - - - +
118C TYR* 3.8 25.0 + - + -
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Residues in contact with GLU 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A THR* 5.0 2.3 + - - -
26A GLY* 4.5 4.9 - - - -
47A GLU* 3.5 16.4 + - + +
48A GLY* 3.8 5.7 - - - -
68A LEU* 3.3 54.3 - - + +
69A SER* 3.1 23.6 + - - -
103C ARG* 3.0 16.4 + - + +
104C TYR* 3.1 19.3 + - - +
106C GLU* 1.3 76.6 - - - +
108C TRP* 1.3 58.3 + - + +
109C GLY 3.2 3.7 + - - -
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Residues in contact with TRP 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A GLY* 4.6 2.0 - - - -
49A LEU 5.5 0.6 + - - -
66A GLN 4.4 0.9 - - - -
69A SER* 2.8 31.3 + - - -
1002A CL 3.7 17.5 - - + +
101C LEU* 5.3 0.7 - - + -
104C TYR* 3.0 48.6 + + + +
105C LEU* 3.8 23.8 - - + +
106C GLU 3.1 0.8 - - - -
107C GLU* 1.3 84.2 - - + +
109C GLY* 1.3 59.9 + - - +
110C GLY 3.3 0.8 + - - -
120C LEU* 4.0 8.5 - - + +
121C PRO* 5.0 4.0 - - - +
155C TRP* 3.6 29.2 - + + -
158C ARG* 3.3 65.0 - - + +
159C ILE* 3.8 25.6 - - + -
161C PHE* 5.7 0.7 - + - -
162C ALA* 4.2 5.2 - - + -
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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