Contacts of the helix formed by residues 111 - 122 (chain A) in PDB entry 4GFU
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 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A LYS* 3.9 42.6 - - + +
87A ILE* 5.0 6.4 - - + +
105A GLN* 4.3 5.7 + - - -
107A PRO* 3.7 6.5 - - - +
108A LEU* 3.0 31.5 + - + +
110A HIS* 1.3 90.8 - - + +
112A LEU* 1.3 59.5 + - - +
113A LEU 3.2 2.2 - - - -
114A ASP* 3.1 19.6 + - - +
115A PHE* 2.9 27.7 + - - +
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Residues in contact with LEU 112 (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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107A PRO* 3.6 24.7 - - + -
108A LEU 3.2 14.4 + - - +
109A PRO* 3.9 14.1 - - + +
110A HIS 3.6 1.2 - - - -
111A THR* 1.3 78.2 - - - +
113A LEU* 1.3 63.4 + - - +
115A PHE* 3.2 6.2 + - - +
116A TRP* 3.1 28.4 + - + +
142A GLU* 4.0 17.0 - - + +
143A ARG 3.8 16.2 - - - +
144A TYR* 3.7 24.2 - - + -
152A LEU* 4.8 9.4 - - + -
154A THR* 3.7 22.7 - - + +
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Residues in contact with LEU 113 (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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78A LEU* 5.2 5.6 - - + -
83A HIS* 4.0 29.2 - - + +
110A HIS 5.1 4.1 + - - +
111A THR 3.2 0.6 - - - -
112A LEU* 1.3 81.3 - - - +
114A ASP* 1.3 60.8 + - - +
116A TRP* 3.4 1.7 + - - -
117A ARG* 2.9 35.0 + - + +
154A THR* 3.3 26.0 - - + +
155A GLY* 4.5 13.9 - - - +
156A LEU 4.8 2.0 - - - +
157A PHE* 3.6 30.7 - - + -
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Residues in contact with ASP 114 (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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59A LYS* 4.4 12.6 + - - +
75A LEU* 3.6 8.1 - - + +
83A HIS* 5.3 1.6 + - - -
84A SER* 6.5 0.7 - - - -
86A TYR 3.9 15.7 - - - +
87A ILE* 3.6 19.9 - - + +
110A HIS 4.5 3.9 - - - +
111A THR* 3.1 28.3 + - - +
113A LEU* 1.3 78.3 - - - +
115A PHE* 1.3 65.6 + - - +
117A ARG* 3.0 34.8 + - - +
118A LEU 3.0 18.7 + - - -
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Residues in contact with PHE 115 (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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87A ILE* 3.7 15.0 - - + +
104A THR* 4.3 15.5 - - + -
105A GLN 5.0 0.9 - - - -
107A PRO* 3.9 31.9 - - + -
111A THR 2.9 12.5 + - - +
112A LEU* 3.3 9.4 - - - +
114A ASP* 1.3 76.1 - - - +
116A TRP* 1.3 71.0 + + - +
118A LEU* 3.2 7.9 + - + +
119A VAL* 3.0 43.9 + - + +
127A ILE* 4.0 20.6 - - + -
144A TYR* 3.6 46.4 - + + -
226A CYS* 4.1 17.3 - - - -
228A HIS* 4.4 5.2 - + - -
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Residues in contact with TRP 116 (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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112A LEU* 3.1 24.5 + - + +
113A LEU* 3.9 1.8 - - - +
115A PHE* 1.3 82.9 - + - +
117A ARG* 1.3 66.8 + - - +
119A VAL* 3.2 32.4 + - + +
120A TRP* 2.9 27.6 + + + +
127A ILE* 4.4 10.1 - - + -
144A TYR* 3.1 47.2 + + + +
152A LEU* 5.2 0.2 - - - +
154A THR* 4.1 19.9 + - - -
157A PHE* 3.7 25.8 - + + -
159A ILE* 3.7 38.5 - - + +
176A LEU* 4.0 21.1 - - + -
178A VAL* 4.2 17.3 - - + -
187A VAL* 4.6 7.6 - - + -
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Residues in contact with ARG 117 (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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75A LEU* 3.6 39.9 + - + +
76A SER 4.5 0.2 - - - -
77A LEU* 2.8 50.0 + - + +
78A LEU* 4.5 6.2 - - + +
79A GLN* 5.1 0.4 - - - +
83A HIS* 3.8 26.6 + - - +
84A SER* 2.9 30.7 + - - +
86A TYR 5.1 0.2 + - - -
113A LEU* 2.9 42.6 + - + +
114A ASP* 3.0 33.3 + - - +
116A TRP* 1.3 74.8 - - - +
118A LEU* 1.3 58.3 + - - +
121A GLU* 2.9 34.3 + - - +
157A PHE* 4.0 8.0 - - + -
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Residues in contact with LEU 118 (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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73A VAL* 4.2 9.4 - - + -
75A LEU* 3.6 17.4 - - + +
87A ILE* 3.8 31.6 - - + -
102A ILE* 3.7 46.7 - - + -
104A THR* 4.6 12.1 - - + -
114A ASP 3.0 12.1 + - - +
115A PHE* 3.3 9.6 - - + +
117A ARG* 1.3 74.2 - - - +
119A VAL* 1.3 80.3 + - + +
122A PHE* 3.2 29.8 + - + +
124A VAL* 4.5 3.1 - - + -
226A CYS* 4.3 11.9 - - - -
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Residues in contact with VAL 119 (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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115A PHE* 3.0 44.2 + - + +
116A TRP* 3.2 30.7 + - + +
118A LEU* 1.3 87.2 - - + +
120A TRP* 1.3 62.9 + - + +
123A GLY* 3.4 1.6 + - - -
124A VAL* 3.0 55.2 + - + +
127A ILE* 4.1 12.1 - - + -
178A VAL* 5.9 1.3 - - + -
185A ARG* 4.5 0.5 + - - -
187A VAL* 4.1 12.8 - - + -
226A CYS* 5.0 1.8 - - - -
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Residues in contact with TRP 120 (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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77A LEU* 3.8 23.5 - - + +
116A TRP* 2.9 17.2 + - + +
117A ARG 3.9 2.2 - - - +
119A VAL* 1.3 77.6 - - + +
121A GLU* 1.3 69.1 + - - +
123A GLY* 3.2 3.6 + - - -
157A PHE* 3.7 24.9 - + + -
178A VAL* 3.5 34.1 - - + -
180A PHE* 3.6 31.1 - + + -
183A GLU* 3.5 45.4 + - + -
185A ARG* 2.8 72.8 + - + +
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Residues in contact with GLU 121 (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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74A ILE 3.8 2.3 - - - +
75A LEU* 3.4 8.7 - - - +
76A SER* 2.8 46.9 + - - -
77A LEU* 3.1 20.0 + - + +
117A ARG 2.9 21.6 + - - +
120A TRP* 1.3 79.4 - - - +
122A PHE* 1.3 92.4 + - + +
123A GLY 3.4 2.1 + - - -
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Residues in contact with PHE 122 (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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73A VAL* 3.7 21.8 - - + -
74A ILE 3.6 19.7 - - - -
75A LEU* 4.2 5.6 - - + -
91A PHE* 3.6 28.5 - + - -
102A ILE* 4.2 15.5 - - + -
118A LEU 3.2 21.2 + - - +
121A GLU* 1.3 103.0 - - + +
123A GLY* 1.3 63.7 + - - +
124A VAL* 3.2 5.0 + - + -
223A GLU* 3.8 5.8 - - - +
224A PRO* 3.5 34.0 - - + +
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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