Contacts of the helix formed by residues 115 - 123 (chain B) in PDB entry 4C48
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 115 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B HIS* 3.9 2.9 - - - -
106B VAL 4.6 3.8 - - - -
107B ASN* 4.0 23.3 - - - +
108B ALA 3.5 2.7 - - - +
109B LYS* 5.1 3.4 - - + -
113B GLY 4.4 5.2 - - - +
114B ILE* 1.3 82.6 - - - +
116B PRO* 1.3 73.3 - - - +
117B LEU* 3.2 13.0 + - - +
118B HIS* 3.2 32.0 + - - +
119B LEU* 3.1 18.2 + - - +
141B ALA* 3.7 26.7 - - + +
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Residues in contact with PRO 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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84B LEU* 3.7 48.2 - - + +
85B HIS* 3.5 20.9 - - + +
88B ALA* 3.4 11.5 - - + +
105B ASP 4.7 2.0 - - - +
106B VAL 3.4 18.4 - - - +
108B ALA* 3.3 17.0 - - + +
115B THR* 1.3 84.2 - - - +
117B LEU* 1.3 56.2 + - - +
119B LEU* 4.3 3.4 - - + -
120B ALA* 2.9 31.9 + - - +
132B LEU* 3.7 9.2 - - + -
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Residues in contact with LEU 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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106B VAL* 4.8 2.8 + - - +
115B THR* 3.1 10.7 - - - +
116B PRO* 1.3 77.0 - - - +
118B HIS* 1.3 62.2 + - + +
120B ALA* 3.4 1.2 + - - +
121B ALA* 2.8 32.2 + - - +
129B VAL* 3.7 18.8 - - + +
132B LEU* 3.6 14.3 - - + +
133B LEU* 3.5 32.3 - - + -
137B ALA* 4.4 15.5 - - + -
138B ASP 3.2 29.2 - - - +
139B VAL* 3.7 15.7 - - + -
141B ALA* 5.5 0.9 - - + +
148B THR* 5.6 0.2 - - + -
149B ALA* 3.6 23.8 - - + +
165B LEU* 4.4 0.7 - - + -
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Residues in contact with HIS 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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113B GLY 3.8 6.1 + - - -
114B ILE* 4.0 10.0 - - + -
115B THR* 3.2 34.2 + - - +
117B LEU* 1.3 78.8 - - + +
119B LEU* 1.3 64.1 + - - +
121B ALA 3.0 10.2 + - - -
122B ASN* 3.0 11.7 + - - +
141B ALA* 2.6 36.1 + - + +
142B GLN 3.8 0.7 - - - -
143B ASP* 3.4 28.0 - - + +
147B LYS 2.9 13.2 + - - -
148B THR* 3.4 6.0 - - - -
149B ALA* 3.1 30.9 + - + -
152B ILE* 3.1 21.8 - - + +
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Residues in contact with LEU 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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808A ARG* 5.8 12.1 - - - +
85B HIS* 3.7 45.1 - - + +
86B LEU* 6.3 0.2 - - + -
88B ALA* 4.8 0.4 - - + -
89B HIS* 3.2 47.5 + - + +
110B ASP* 6.0 0.4 - - - +
114B ILE* 3.9 15.9 - - + -
115B THR 3.1 11.4 + - - +
116B PRO* 3.8 5.8 - - + +
118B HIS* 1.3 81.9 - - - +
120B ALA* 1.3 62.8 + - - +
122B ASN* 3.1 16.6 + - + +
123B ARG* 3.5 8.7 + - - +
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Residues in contact with ALA 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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88B ALA* 3.5 23.5 + - + +
89B HIS* 5.0 0.2 - - - +
116B PRO 2.9 18.9 + - - +
117B LEU 4.0 2.2 - - - +
119B LEU* 1.3 77.2 - - - +
121B ALA* 1.3 62.9 + - - +
122B ASN 3.1 1.0 + - - -
123B ARG 3.5 8.0 + - - -
124B GLY 3.7 0.2 + - - -
125B HIS* 3.7 25.4 + - + +
128B ILE* 3.9 25.8 - - + -
129B VAL* 4.6 7.4 - - - +
132B LEU* 4.0 6.7 - - + -
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Residues in contact with ALA 121 (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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117B LEU 2.8 19.1 + - - +
118B HIS 3.0 7.6 + - - +
120B ALA* 1.3 77.0 - - - +
122B ASN* 1.3 57.9 + - - +
124B GLY 4.2 1.3 + - - -
129B VAL* 4.6 10.3 - - + +
149B ALA* 3.6 33.0 - - + +
152B ILE* 4.0 10.3 - - + +
156B ASN* 4.3 1.7 + - - -
161B LEU* 3.0 37.5 - - + +
165B LEU* 4.6 1.3 - - + -
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Residues in contact with ASN 122 (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 HIS* 6.0 1.1 - - + +
118B HIS 3.0 9.3 + - - +
119B LEU* 3.6 13.7 - - + +
120B ALA 3.1 0.6 - - - -
121B ALA* 1.3 78.9 - - - +
123B ARG* 1.3 58.6 + - - +
124B GLY 3.3 3.6 + - - -
152B ILE* 3.8 25.9 - - + +
156B ASN* 3.1 30.6 + - - +
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Residues in contact with ARG 123 (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 HIS* 3.6 46.2 - - + +
119B LEU 3.5 5.7 + - - +
120B ALA 3.5 0.8 + - - -
122B ASN* 1.3 77.0 - - - +
124B GLY* 1.3 63.9 + - - +
125B HIS* 3.6 17.2 + - + +
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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