Contacts of the helix formed by residues 108 - 121 (chain B) in PDB entry 4F4I
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 108 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102B GLY* 3.0 13.3 + - - -
106B GLY 3.5 1.4 - - - -
107B ILE* 1.3 78.4 - - - +
109B VAL* 1.3 67.7 + - - -
110B GLU 3.3 2.2 - - - -
111B GLU* 3.2 10.5 + - - +
112B VAL* 3.0 24.6 + - - +
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Residues in contact with VAL 109 (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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98B LEU* 3.2 36.6 - - + +
102B GLY* 4.1 7.4 + - - -
103B TYR* 4.4 23.1 - - + +
108B GLY* 1.3 71.8 - - - +
110B GLU* 1.3 77.0 + - + +
112B VAL 3.2 0.3 + - - -
113B ARG* 2.9 42.4 + - - +
166B GLY 6.1 0.4 - - - +
169B GLU* 5.7 6.7 - - + +
170B ILE* 5.3 8.3 - - + -
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Residues in contact with GLU 110 (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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108B GLY 3.3 0.4 - - - -
109B VAL* 1.3 94.0 - - + +
111B GLU* 1.3 61.5 + - + +
113B ARG* 3.5 28.9 + - - +
114B ALA* 2.9 29.1 + - - +
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Residues in contact with GLU 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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60B ARG* 2.9 34.1 + - - +
107B ILE* 3.1 29.5 - - + +
108B GLY* 3.2 11.9 + - - +
110B GLU* 1.3 75.8 - - + +
112B VAL* 1.3 58.6 + - - +
114B ALA* 3.2 9.0 - - - +
115B LEU* 3.0 26.2 + - - +
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Residues in contact with VAL 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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63B ALA* 5.5 3.8 - - + -
97B SER* 3.7 28.9 - - - +
98B LEU* 3.9 5.8 - - + +
101B GLN* 4.3 7.4 - - + -
102B GLY* 3.6 18.2 - - - +
107B ILE* 3.5 25.8 - - + -
108B GLY 3.0 16.5 + - - +
109B VAL 3.6 3.8 - - - +
111B GLU* 1.3 73.0 - - - +
113B ARG* 1.3 58.8 + - - +
115B LEU* 3.5 12.6 - - + +
116B ASN* 2.7 52.7 + - - +
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Residues in contact with ARG 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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94B ILE* 4.7 5.0 - - + +
95B ASP* 5.8 0.2 + - - -
98B LEU* 3.3 38.0 - - + +
109B VAL* 2.9 26.1 + - - +
110B GLU* 3.5 33.5 + - - +
112B VAL* 1.3 74.2 - - - +
114B ALA* 1.3 54.7 + - - +
116B ASN* 3.5 4.2 - - - +
117B GLU* 2.7 63.1 + - - +
124B TYR* 4.1 20.4 + - - +
170B ILE* 5.0 11.9 + - - +
174B GLU* 4.6 21.6 + - - +
177B ARG* 5.4 4.4 - - - +
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Residues in contact with ALA 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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110B GLU 2.9 14.2 + - - +
111B GLU* 3.2 12.1 - - - +
113B ARG* 1.3 71.1 - - - +
115B LEU* 1.3 70.7 + - - +
117B GLU* 3.0 23.2 + - - +
118B PHE* 3.2 11.0 + - - +
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Residues in contact with LEU 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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63B ALA* 3.6 43.5 - - + +
64B MET* 3.6 30.3 - - + +
67B ALA* 4.0 12.8 - - + -
111B GLU 3.0 15.0 + - - +
112B VAL* 3.5 14.4 - - + +
114B ALA* 1.3 73.2 - - - +
116B ASN* 1.3 69.3 + - - +
118B PHE* 3.0 25.4 + - + +
119B ALA* 3.3 6.9 + - - +
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Residues in contact with ASN 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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67B ALA* 4.1 13.1 - - - +
70B ARG* 3.1 31.1 + - - -
94B ILE* 3.3 33.9 + - + +
97B SER* 3.6 10.7 - - - -
98B LEU* 5.2 0.4 - - - +
112B VAL* 2.7 50.5 + - - +
113B ARG 3.9 0.4 - - - +
114B ALA 3.2 0.2 - - - -
115B LEU* 1.3 77.5 - - - +
117B GLU* 1.3 64.1 + - - +
119B ALA* 3.2 6.3 + - - +
120B ILE* 3.1 29.7 + - + +
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Residues in contact with GLU 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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94B ILE* 5.2 0.7 - - + -
113B ARG* 2.7 49.4 + - - +
114B ALA* 3.0 11.2 + - - +
116B ASN* 1.3 71.9 - - - +
118B PHE* 1.3 56.8 + - - +
120B ILE* 3.9 5.5 - - - -
121B ASN* 3.1 27.4 + - - -
122B GLY* 3.9 6.1 + - - +
124B TYR* 3.4 31.6 + - + +
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Residues in contact with PHE 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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71B ARG* 4.7 9.2 + - - -
114B ALA 3.2 8.9 + - - +
115B LEU* 3.0 18.5 + - + +
117B GLU* 1.3 77.7 - - - +
119B ALA* 1.3 65.6 + - + +
120B ILE 3.4 0.7 + - - -
121B ASN* 3.7 10.0 + - - +
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Residues in contact with ALA 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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67B ALA* 3.6 42.6 - - + +
68B ALA* 5.4 0.2 - - - -
70B ARG* 5.4 0.7 - - + -
71B ARG* 2.9 44.5 + - + +
74B LEU* 4.4 0.9 - - - +
115B LEU 3.3 3.3 + - - +
116B ASN* 3.2 10.9 + - - +
118B PHE* 1.3 83.8 - - + +
120B ILE* 1.3 65.5 + - + +
121B ASN 3.6 0.2 - - - -
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Residues in contact with ILE 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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70B ARG* 4.2 19.1 - - + -
71B ARG* 4.4 0.2 - - - -
74B LEU* 3.8 14.7 - - + +
93B TYR* 3.2 38.6 - - + +
94B ILE* 4.4 15.9 - - + -
116B ASN* 3.1 24.1 + - + +
117B GLU* 4.2 4.5 - - - +
119B ALA* 1.3 82.6 - - + +
121B ASN* 1.3 59.9 + - - +
122B GLY 4.3 1.6 - - - +
123B LEU* 2.7 64.9 + - - +
124B TYR* 4.0 18.4 - - + +
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Residues in contact with ASN 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ARG* 3.9 26.2 - - - +
117B GLU 3.1 11.9 + - - -
118B PHE 3.7 6.9 + - - +
119B ALA 3.6 1.4 - - - -
120B ILE* 1.3 77.6 - - - +
122B GLY* 1.3 59.7 + - - +
123B LEU* 5.2 0.3 - - - +
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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