Contacts of the helix formed by residues 110 - 120 (chain B) in PDB entry 3P05
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 110 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109B SER* 1.3 76.5 - - - +
111B LEU* 1.3 65.3 + - - +
112B GLN* 3.3 18.2 + - - +
113B GLU* 2.9 40.6 + - - +
114B GLN* 3.0 25.1 + - - +
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Residues in contact with LEU 111 (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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12B HIS* 3.8 34.8 - - + +
48B THR* 4.2 8.5 - - + +
50B GLN* 3.4 43.7 - - - +
109B SER 4.3 0.2 + - - -
110B THR* 1.3 73.5 - - - +
112B GLN* 1.3 71.4 + - + +
114B GLN* 3.3 19.2 + - - +
115B ILE* 3.0 48.7 + - + +
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Residues in contact with GLN 112 (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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96B MET* 5.2 0.2 - - - +
110B THR* 3.0 18.1 - - - +
111B LEU* 1.3 88.6 + - + +
113B GLU* 1.3 64.6 + - - +
115B ILE* 3.4 8.4 + - + +
116B GLY* 3.0 19.8 + - - -
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Residues in contact with GLU 113 (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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96B MET* 3.6 25.5 - - + +
97B ARG* 2.7 43.8 + - - +
108B THR 4.6 0.2 - - - +
109B SER* 3.5 1.2 - - - -
110B THR* 2.9 46.3 + - - +
112B GLN* 1.3 76.9 - - + +
114B GLN* 1.3 64.4 + - - +
116B GLY 3.2 1.0 + - - -
117B TRP* 3.1 38.9 + - + -
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Residues in contact with GLN 114 (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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48B THR* 3.8 8.6 - - - -
49B PRO* 3.6 29.6 - - + +
50B GLN* 3.0 34.6 + - - +
103B ASP 4.6 1.6 - - - +
106B GLY* 3.6 18.8 + - - -
109B SER* 3.1 38.0 + - - +
110B THR 3.0 17.3 + - - +
111B LEU* 3.6 9.4 - - - +
112B GLN 3.2 0.2 - - - -
113B GLU* 1.3 76.1 - - - +
115B ILE* 1.3 64.4 + - - +
117B TRP* 3.4 12.8 + - + +
118B MET* 3.1 28.6 + - - +
126B VAL* 4.1 1.0 - - - +
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Residues in contact with ILE 115 (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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2B ILE* 4.6 11.9 - - + -
10B MET 5.5 2.7 - - - +
11B VAL* 5.6 1.6 - - - +
12B HIS* 3.6 42.8 - - + +
48B THR* 4.8 1.8 - - + -
111B LEU* 3.0 34.3 + - + +
112B GLN* 3.7 7.4 - - + +
114B GLN* 1.3 74.8 - - - +
116B GLY* 1.3 68.1 + - - +
118B MET* 3.2 1.5 + - - +
119B THR* 2.8 43.8 + - + +
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Residues in contact with GLY 116 (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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96B MET* 4.0 17.0 - - - -
112B GLN 3.0 14.2 + - - -
113B GLU 3.2 4.2 + - - -
115B ILE* 1.3 76.9 - - - +
117B TRP* 1.3 56.5 + - - +
119B THR* 3.6 4.0 + - - -
120B HIS* 2.9 32.7 + - - +
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Residues in contact with TRP 117 (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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96B MET* 3.8 25.9 - - + +
97B ARG* 3.0 39.5 + - + -
98B GLU 4.2 1.1 - - - -
99B PRO* 3.6 35.6 - - + +
103B ASP* 3.9 20.9 - - + -
109B SER* 4.1 16.2 - - - -
113B GLU* 3.1 41.3 + - + -
114B GLN* 3.7 10.8 - - + +
116B GLY* 1.3 76.1 - - - +
118B MET* 1.3 60.5 + - - +
119B THR 3.4 0.3 + - - -
120B HIS* 3.5 11.4 - + + +
124B ILE* 2.8 61.0 + - + +
126B VAL* 4.1 17.0 - - + -
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Residues in contact with MET 118 (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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2B ILE* 3.5 31.4 - - + +
10B MET* 5.3 5.2 - - - +
46B GLY* 3.7 15.5 - - - +
47B ALA 3.5 21.1 - - - +
48B THR* 3.8 27.6 - - + -
49B PRO* 4.0 2.2 - - - -
114B GLN 3.1 20.9 + - - +
115B ILE 3.2 1.0 + - - +
117B TRP* 1.3 77.4 - - - +
119B THR* 1.3 61.0 + - - +
120B HIS 3.5 0.2 - - - -
123B PRO* 3.4 18.6 - - - +
124B ILE 3.6 9.2 - - - +
125B PRO* 4.5 5.3 - - + +
126B VAL* 3.6 26.2 - - + +
127B GLY* 4.1 6.1 - - - +
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Residues in contact with THR 119 (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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2B ILE* 3.9 19.7 - - + -
10B MET* 3.0 53.2 + - + +
115B ILE* 2.8 31.3 + - + +
116B GLY* 3.6 3.6 + - - -
118B MET* 1.3 79.1 - - - +
120B HIS* 1.3 70.2 + - - +
121B ASN* 3.7 2.8 + - - +
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Residues in contact with HIS 120 (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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96B MET* 5.7 10.1 - - + -
116B GLY 2.9 18.7 + - - +
117B TRP* 3.5 15.0 - + - +
118B MET 3.5 0.4 - - - -
119B THR* 1.3 83.1 - - - +
121B ASN* 1.3 78.5 + - - +
122B PRO* 2.7 30.9 + - + +
123B PRO* 3.0 21.5 - - - +
124B ILE* 4.7 8.9 - - + +
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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