Contacts of the helix formed by residues 111 - 125 (chain E) in PDB entry 6G2T
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 PRO 111 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193D THR 3.4 17.5 - - - +
194D GLU 3.0 15.3 - - - +
195D ARG 4.4 1.1 - - - -
196D GLY* 3.7 19.5 - - - +
198D SER* 6.0 0.9 - - - +
74E ILE* 3.3 22.7 - - + -
109E LEU 4.1 2.0 - - - +
110E ASN* 1.4 104.2 - - - +
112E LYS* 1.3 65.2 + - - +
113E ALA* 3.3 5.8 - - + +
114E ASN* 3.3 25.6 + - - +
115E ARG* 3.8 6.8 + - - -
176E ARG* 4.4 4.0 - - - +
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Residues in contact with LYS 112 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194D GLU* 2.6 51.3 + - + +
195D ARG* 5.9 0.4 - - - -
255D ARG* 5.3 2.9 - - - +
110E ASN 3.7 1.2 + - - +
111E PRO* 1.3 70.0 - - - +
113E ALA* 1.3 64.8 + - - +
115E ARG 3.3 2.3 + - - -
116E GLU* 3.2 41.1 + - - +
370E HIS* 3.3 53.7 + - + +
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Residues in contact with ALA 113 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194D GLU 4.4 1.2 + - - -
195D ARG 6.0 2.7 - - - +
78E TRP* 5.0 1.6 - - + -
111E PRO* 3.3 6.1 - - + -
112E LYS* 1.3 80.2 - - - +
114E ASN* 1.3 58.8 + - - +
116E GLU* 3.9 9.6 - - - +
117E LYS* 2.9 35.0 + - + +
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Residues in contact with ASN 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E GLY 4.8 1.1 - - - +
74E ILE* 3.2 30.7 - - - +
75E VAL* 3.3 32.5 + - + +
78E TRP* 3.5 14.8 - - + -
106E GLU* 4.1 7.9 - - - +
110E ASN* 3.1 28.7 + - - +
111E PRO* 3.3 15.3 + - - +
112E LYS 3.3 0.8 - - - -
113E ALA* 1.3 78.0 - - - +
115E ARG* 1.3 61.6 + - - +
118E MET* 3.2 29.2 + - + +
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Residues in contact with ARG 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106E GLU* 3.3 48.1 + - + +
107E ALA 3.6 13.9 + - - -
109E LEU* 4.7 4.0 - - - +
110E ASN* 3.1 27.5 + - - +
111E PRO 3.8 3.6 + - - +
112E LYS 3.3 7.8 + - - +
114E ASN* 1.3 77.3 - - - +
116E GLU* 1.3 63.1 + - - +
118E MET* 3.5 4.6 + - - +
119E THR* 3.3 29.5 + - - +
133E VAL* 5.1 7.5 - - + +
135E ILE* 4.1 15.4 - - - +
369E VAL* 4.0 23.1 - - + -
370E HIS* 3.7 30.1 + - + +
373E CYS* 6.3 0.2 - - - -
374E PHE* 4.1 25.6 + - - -
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Residues in contact with GLU 116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112E LYS* 3.2 30.4 + - - +
113E ALA* 3.9 8.0 - - - +
115E ARG* 1.3 73.4 - - - +
117E LYS* 1.3 63.3 + - - +
119E THR* 2.9 20.2 + - - -
120E GLN* 3.1 13.6 + - - +
366E PRO* 3.9 29.1 - - + +
367E SER* 4.1 18.3 - - - +
369E VAL* 4.8 1.8 - - + -
370E HIS* 3.6 25.2 + - + -
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Residues in contact with LYS 117 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E TRP* 3.3 47.8 - - + +
113E ALA 2.9 17.5 + - - +
116E GLU* 1.3 75.4 - - - +
118E MET* 1.3 60.5 - - - +
120E GLN* 3.1 34.3 + - - +
121E ILE* 2.8 49.7 + - + +
201K SER* 3.2 29.5 + - - +
202K LYS* 4.0 13.1 - - - +
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Residues in contact with MET 118 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E ASN* 5.9 6.3 - - + -
75E VAL* 5.7 8.1 - - + -
78E TRP* 3.8 16.5 - - + -
85E TRP* 3.7 23.0 - - + -
104E LEU* 3.6 39.3 - - + -
105E THR 4.9 11.0 - - - +
106E GLU* 4.1 20.6 - - - +
114E ASN* 3.2 26.2 + - + +
115E ARG* 3.7 4.7 - - - +
116E GLU 3.3 0.2 - - - -
117E LYS* 1.3 76.9 - - - +
119E THR* 1.3 62.6 + - + +
121E ILE* 3.6 2.9 + - - +
122E MET* 3.1 25.3 + - - +
133E VAL* 4.5 11.0 - - + -
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Residues in contact with THR 119 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115E ARG 3.3 8.8 + - - +
116E GLU* 2.9 20.3 + - - -
118E MET* 1.3 74.6 - - - +
120E GLN* 1.3 58.7 + - - +
122E MET 3.2 1.0 + - - -
123E PHE* 2.8 52.3 + - + -
131E MET* 3.7 24.0 - - + -
133E VAL* 4.2 16.4 - - + -
356E ILE* 4.9 2.9 - - + -
361E TYR* 4.5 0.8 - - - -
366E PRO* 4.0 7.6 + - - +
369E VAL* 3.3 35.3 - - + +
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Residues in contact with GLN 120 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116E GLU 3.1 10.5 + - - +
117E LYS* 3.1 42.7 + - - +
119E THR* 1.3 81.3 + - - +
121E ILE* 1.3 63.1 + - - +
124E GLU* 3.0 40.7 + - - +
361E TYR* 3.3 26.4 + - + +
366E PRO* 4.4 13.1 - - + +
197K VAL* 4.6 12.1 - - - +
198K ASP 5.3 1.0 + - - +
201K SER* 4.0 17.4 + - - -
202K LYS* 4.4 10.1 - - - +
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Residues in contact with ILE 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E TRP* 3.3 51.1 - - + +
82E GLU* 4.9 7.6 - - + -
85E TRP* 3.7 28.3 - - + -
117E LYS* 2.8 37.1 + - - +
118E MET 3.9 4.0 - - - +
120E GLN* 1.3 75.8 - - - +
122E MET* 1.3 58.7 + - - +
124E GLU* 5.5 0.2 - - - -
125E THR* 2.7 61.1 + - + +
126E PHE* 3.5 3.3 + - + -
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Residues in contact with MET 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E ILE* 5.0 0.2 - - + -
85E TRP* 3.3 55.9 - - + +
89E PHE* 4.4 14.6 - - + -
102E VAL* 4.0 23.6 - - + -
104E LEU* 3.7 14.6 - - + -
118E MET 3.1 14.1 + - - +
119E THR 3.2 0.4 + - - -
121E ILE* 1.3 79.6 - - - +
123E PHE* 1.3 54.4 + - - +
126E PHE* 2.4 41.8 - - + +
128E THR* 3.5 14.3 - - + +
131E MET* 3.3 34.1 - - + -
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Residues in contact with PHE 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119E THR* 2.8 38.6 + - - +
122E MET* 1.3 74.0 - - - +
124E GLU* 1.3 59.8 + - - +
126E PHE 3.5 7.6 - - - +
127E ASN* 4.2 5.4 - - - +
128E THR* 4.5 9.2 - - + -
130E ALA 4.9 0.4 - - - -
131E MET* 3.3 37.0 - - + -
356E ILE* 3.6 33.0 - - + -
357E SER 3.7 1.8 - - - -
358E LYS* 3.4 62.5 - - + +
361E TYR* 3.2 50.3 - + + -
369E VAL* 5.9 0.7 - - + -
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Residues in contact with GLU 124 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120E GLN* 3.0 27.5 + - - +
123E PHE* 1.3 79.6 - - - +
125E THR* 1.3 65.6 + - - +
126E PHE 3.4 3.7 - - - -
127E ASN* 4.9 1.6 + - - +
358E LYS* 6.1 1.8 - - - +
361E TYR* 4.0 26.2 + - + +
362E ASP* 6.0 0.7 - - - +
197K VAL* 4.3 21.7 - - - +
202K LYS* 5.9 2.8 + - - +
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Residues in contact with THR 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82E GLU* 3.7 27.0 - - + +
121E ILE* 2.7 41.8 + - - +
124E GLU* 1.3 74.7 - - - +
126E PHE* 1.3 79.5 + - + -
127E ASN 4.4 0.2 + - - -
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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