Contacts of the helix formed by residues 95 - 105 (chain B) in PDB entry 3A4T
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 95 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92B ALA 3.0 17.7 + - - -
94B PRO* 1.4 76.5 - - - +
96B GLY* 1.3 63.0 + - - +
97B LYS 3.4 2.5 - - - -
98B THR* 3.7 7.9 - - - -
99B THR* 2.8 35.2 + - - +
124B LEU* 3.6 15.7 - - - -
127B ASN* 4.6 7.1 - - - +
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Residues in contact with GLY 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ARG* 2.7 27.6 + - - -
66B MET* 3.9 26.0 - - - +
68B GLN* 4.2 14.1 - - - -
94B PRO* 3.8 1.6 - - - +
95B GLY* 1.3 78.5 - - - +
97B LYS* 1.3 59.2 + - - +
99B THR* 3.1 3.6 + - - -
100B HIS* 3.2 4.0 + - - +
501B SFG 3.1 11.9 + - - -
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Residues in contact with LYS 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B GLN* 5.0 2.0 - - - +
72B SER* 3.4 35.9 - - - +
75B PRO* 3.9 16.2 - - + -
76B PRO* 4.1 5.6 - - + +
89B ASP* 4.4 0.9 - - - -
96B GLY* 1.3 74.1 - - - +
98B THR* 1.3 60.4 + - - +
100B HIS* 3.5 7.6 - - - +
101B LEU* 2.9 33.7 + - - +
161B LEU* 3.5 21.8 - - + -
163B ASP* 2.6 47.8 + - + +
266B PHE* 3.7 20.7 - - - -
501B SFG 2.9 32.0 + - - +
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Residues in contact with THR 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B ASP* 2.3 31.6 + - - +
92B ALA* 3.7 18.6 + - - +
95B GLY* 3.5 10.6 + - - -
96B GLY 3.5 0.8 - - - -
97B LYS* 1.3 76.9 - - - +
99B THR* 1.3 59.1 + - - +
101B LEU* 3.6 5.9 + - - +
102B ALA* 3.0 25.8 + - - +
111B ILE* 3.7 27.6 - - + +
113B ALA* 3.7 15.0 - - + -
124B LEU* 4.0 1.6 - - - +
128B ILE* 4.2 9.8 - - + +
136B THR* 4.1 14.1 + - + +
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Residues in contact with THR 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ARG* 3.2 13.8 + - - -
16B ASN* 5.2 0.7 - - - +
18B LEU* 4.9 0.9 - - - +
66B MET* 4.4 2.3 - - - -
95B GLY 2.8 22.9 + - - +
96B GLY* 3.1 9.2 + - - -
98B THR* 1.3 73.9 - - - +
100B HIS* 1.3 59.4 + - - +
102B ALA* 3.8 1.6 - - - +
103B GLN* 2.9 29.5 + - - +
127B ASN* 3.9 9.6 - - + +
128B ILE* 3.4 26.9 - - + +
131B MET* 3.9 30.5 - - + +
133B VAL* 3.7 21.9 - - + +
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Residues in contact with HIS 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ARG* 3.4 27.5 - - - +
41B LEU* 4.6 1.0 - - - +
43B TYR* 3.2 23.8 - + - -
68B GLN* 4.7 2.7 - - - -
72B SER 4.7 1.8 - - - -
73B MET* 3.4 26.3 + - + +
76B PRO* 3.2 22.9 - - + -
77B ILE* 3.0 37.1 - - + +
96B GLY 3.2 15.8 + - - +
97B LYS* 3.5 8.7 - - - +
99B THR* 1.3 73.6 + - - +
101B LEU* 1.3 66.3 + - - +
103B GLN* 3.2 6.0 + - - +
104B LEU* 2.9 31.0 + - + +
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Residues in contact with LEU 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B PRO* 3.7 26.0 - - + +
79B LEU* 4.0 13.9 - - + -
81B PRO* 3.8 24.7 - - + -
87B ILE* 4.0 20.9 - - + -
89B ASP* 4.5 9.6 - - + -
97B LYS 2.9 21.3 + - - +
98B THR* 3.7 10.5 - - - +
100B HIS* 1.3 74.8 - - - +
102B ALA* 1.3 62.8 + - - +
104B LEU* 3.1 8.2 + - - +
105B MET* 3.1 30.0 + - - +
111B ILE* 3.8 13.7 - - + -
161B LEU* 3.9 23.6 - - + -
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Residues in contact with ALA 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B LEU* 4.4 2.5 - - + -
98B THR 3.0 15.8 + - - +
99B THR 3.4 0.9 + - - +
100B HIS 3.3 0.2 - - - -
101B LEU* 1.3 75.9 - - - +
103B GLN* 1.4 60.9 + - - +
105B MET* 3.1 2.1 + - - -
106B LYS 3.0 4.0 + - - -
107B ASN* 2.9 31.4 + - - +
111B ILE* 3.6 1.9 - - + +
133B VAL* 3.7 29.6 - - + -
135B ASN* 3.5 34.1 - - - +
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Residues in contact with GLN 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ARG* 2.3 48.4 + - - +
15B VAL 2.9 25.0 + - - +
16B ASN* 3.7 7.7 - - - +
17B THR* 3.3 34.3 - - + +
18B LEU* 3.8 26.0 - - + +
43B TYR* 3.8 15.6 - - - -
99B THR 2.9 12.0 + - - +
100B HIS* 3.4 14.1 - - - +
102B ALA* 1.4 74.8 - - - +
104B LEU* 1.3 69.9 + - + +
106B LYS* 3.1 17.3 + - - +
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Residues in contact with LEU 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B TYR* 3.8 25.1 - - + +
76B PRO* 3.4 42.8 - - + +
77B ILE* 3.9 14.1 - - + +
80B ASN* 5.4 1.6 - - - -
81B PRO* 4.1 24.2 - - + +
83B GLU* 4.6 6.4 - - - +
100B HIS* 2.9 18.9 + - + +
101B LEU* 3.1 8.7 + - - +
103B GLN* 1.3 79.9 - - + +
105B MET* 1.3 58.1 + - - +
106B LYS* 3.3 4.7 + - - +
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Residues in contact with MET 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B PRO* 3.7 21.3 - - + -
82B ARG 3.7 14.8 - - - +
83B GLU* 3.6 24.9 - - - +
85B ASP 3.3 26.5 - - - +
87B ILE* 3.9 15.3 - - + -
101B LEU* 3.1 20.0 + - - +
102B ALA 3.1 4.4 + - - +
104B LEU* 1.3 77.4 - - - +
106B LYS* 1.3 70.6 + - - +
107B ASN 3.1 0.2 - - - -
108B LYS* 3.0 44.8 + - - +
110B THR 3.9 9.2 - - - +
111B ILE* 3.9 13.0 - - - -
135B ASN* 3.9 12.3 - - - +
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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
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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