Contacts of the helix formed by residues 97 - 105 (chain A) in PDB entry 3Q1H
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 GLY 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A VAL* 5.7 3.8 - - - -
47A THR* 4.1 3.4 - - - -
96A GLY* 1.3 74.4 + - - -
98A GLY* 1.3 56.5 + - - -
99A ARG 3.2 3.4 - - - -
100A VAL* 2.7 25.4 + - - +
101A TYR* 3.1 15.1 + - - -
124A THR* 5.4 0.7 - - - -
170A SO4 2.8 35.0 + - - -
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Residues in contact with GLY 98 (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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14A VAL* 4.8 2.4 - - - +
97A GLY* 1.3 70.5 - - - -
99A ARG* 1.3 61.7 + - - +
101A TYR* 3.3 15.3 + - - +
102A LYS* 3.0 24.3 + - - +
124A THR* 3.9 25.1 + - - +
125A HIS 4.0 19.7 - - - +
127A PRO* 4.5 2.4 - - - +
170A SO4 5.1 0.6 + - - -
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Residues in contact with ARG 99 (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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44A GLY* 4.2 8.1 - - - -
45A ARG 4.4 0.4 - - - +
63A ILE* 3.5 31.2 + - - +
64A SER* 5.0 0.2 - - - +
97A GLY 3.1 0.6 + - - -
98A GLY* 1.3 74.6 - - - +
100A VAL* 1.3 76.6 + - - +
102A LYS* 3.5 6.5 + - - +
103A GLN* 3.0 57.3 + - - +
124A THR* 5.9 0.2 - - - +
170A SO4 3.5 29.4 + - - +
171A SO4 3.5 32.0 + - - -
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Residues in contact with VAL 100 (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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42A ILE* 5.0 2.7 - - + -
43A MET* 4.6 1.1 - - - -
44A GLY* 3.9 13.0 - - - +
63A ILE* 4.7 11.2 - - + -
79A ILE* 5.6 0.2 - - - -
94A VAL* 3.5 26.0 - - + -
96A GLY 3.4 23.1 - - - +
97A GLY 2.7 14.4 + - - +
99A ARG* 1.3 85.5 - - - +
101A TYR* 1.3 63.2 + - - +
103A GLN* 3.3 6.7 + - - +
104A PHE* 3.0 38.8 + - + -
170A SO4 3.4 16.8 - - - +
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Residues in contact with TYR 101 (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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5A LEU* 4.1 21.5 - - + +
6A ILE 2.6 34.2 + - - -
7A ALA* 3.3 21.0 - - + +
14A VAL* 4.2 19.4 - - + +
22A PRO* 4.4 2.4 - - - +
94A VAL* 3.4 20.2 - - + -
95A MET 3.2 13.7 + - - -
96A GLY* 3.4 20.6 - - - -
97A GLY 3.1 22.0 + - - -
98A GLY* 3.3 10.1 + - - +
100A VAL* 1.3 77.1 - - - +
102A LYS* 1.3 61.6 + - - +
104A PHE* 3.2 2.8 + - - +
105A LEU* 3.1 24.3 + - - +
126A PHE* 3.7 22.4 - + + -
127A PRO* 3.6 18.4 - - + +
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Residues in contact with LYS 102 (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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98A GLY 3.0 17.0 + - - +
99A ARG* 3.8 7.2 - - - +
100A VAL 3.3 0.2 - - - -
101A TYR* 1.3 77.7 - - - +
103A GLN* 1.3 64.5 + - + +
104A PHE 3.4 0.5 + - - -
105A LEU* 3.4 13.9 + - + +
106A ASP* 4.9 0.5 + - - -
127A PRO* 3.8 28.2 - - + +
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Residues in contact with GLN 103 (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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63A ILE* 5.8 0.9 - - - +
79A ILE* 3.4 41.1 + - + +
99A ARG* 3.0 51.4 + - - +
100A VAL* 3.3 5.6 + - - +
101A TYR 3.3 0.2 - - - -
102A LYS* 1.3 77.9 - - + +
104A PHE* 1.3 59.3 + - - +
105A LEU 3.4 0.6 + - - -
106A ASP* 4.9 3.5 + - - +
107A ARG* 4.4 6.2 + - - -
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Residues in contact with PHE 104 (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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3A ILE* 4.2 9.9 - - + -
5A LEU* 3.9 18.6 - - + -
42A ILE* 3.9 36.6 - - + -
63A ILE* 3.9 4.9 - - + -
79A ILE* 3.5 45.3 - - + -
82A ALA* 4.5 0.2 - - + -
83A LEU* 3.6 33.7 - - + -
94A VAL* 3.7 25.6 - - + -
100A VAL* 3.0 28.5 + - + +
101A TYR 3.7 0.4 - - - +
103A GLN* 1.3 76.5 - - - +
105A LEU* 1.3 59.7 + - - +
106A ASP 3.3 2.5 - - - -
107A ARG* 3.1 9.8 + - + +
108A ALA* 2.8 27.7 + - - +
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Residues in contact with LEU 105 (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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5A LEU* 4.0 11.2 - - + -
101A TYR 3.1 14.7 + - - +
102A LYS* 3.4 12.9 + - + +
103A GLN 3.4 0.2 - - - -
104A PHE* 1.3 76.9 - - - +
106A ASP* 1.3 65.9 + - - +
108A ALA* 3.3 14.1 + - - +
111A MET* 3.6 30.7 - - + -
127A PRO* 4.3 13.9 - - + -
128A ASP 3.2 27.8 - - - +
129A TYR* 4.0 12.1 - - + -
134A TRP* 4.0 9.2 - - + +
159A ARG* 2.9 22.2 + - - +
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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