Contacts of the strand formed by residues 109 - 121 (chain E) in PDB entry 1GMO
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 LYS 109 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50E LEU* 3.4 3.2 - - - -
51E ILE* 2.5 53.9 + - + +
53E ILE* 5.6 5.8 - - + +
108E VAL* 1.3 79.1 - - - +
110E LYS* 1.3 64.4 + - - +
111E GLU* 4.0 0.4 + - + -
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Residues in contact with LYS 110 (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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48E THR* 4.6 11.4 - - + -
49E THR 3.5 7.9 - - - +
50E LEU* 4.8 0.7 - - - +
103E SER* 5.6 13.6 + - - +
109E LYS* 1.3 75.9 - - - +
111E GLU* 1.3 62.1 + - - +
118E LEU* 6.3 0.9 - - + -
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Residues in contact with GLU 111 (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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48E THR* 3.7 5.1 - - - +
49E THR* 3.1 42.0 + - + +
51E ILE* 5.4 8.1 - - + -
109E LYS 5.0 2.5 - - - +
110E LYS* 1.3 76.6 - - - +
112E PHE* 1.3 70.3 + - - +
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Residues in contact with PHE 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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47E LYS* 3.2 43.1 - - + -
48E THR* 4.6 1.1 - - - +
49E THR* 4.7 0.3 - - - +
111E GLU* 1.3 80.9 - - - +
113E GLY* 1.3 69.3 + - - +
114E HIS* 3.6 44.9 - + - -
116E PHE* 4.5 5.9 - - - -
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Residues in contact with GLY 113 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47E LYS* 2.7 40.1 + - - -
112E PHE* 1.3 89.2 - - - +
114E HIS* 1.3 61.0 + - - -
115E GLU* 3.4 12.1 - - - -
116E PHE* 3.7 13.9 + - - -
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Residues in contact with HIS 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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47E LYS* 4.5 5.2 - - + +
91E LYS* 2.8 23.7 + - - -
112E PHE* 3.6 33.8 - + - -
113E GLY* 1.3 73.8 - - - +
115E GLU* 1.3 61.7 + - - +
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Residues in contact with GLU 115 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90E ASP* 3.0 31.2 - - - +
91E LYS* 2.8 39.3 + - - +
92E ALA* 3.6 20.4 - - + +
113E GLY* 3.6 5.5 - - - -
114E HIS* 1.3 85.9 + - - +
116E PHE* 1.3 83.5 + - + +
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Residues in contact with PHE 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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47E LYS* 3.1 18.4 + - - -
48E THR 2.8 24.9 - - - +
49E THR* 3.4 30.5 - - + -
88E VAL* 4.0 16.2 - - + -
89E PHE 3.6 1.8 - - - -
90E ASP* 3.2 34.5 - - + -
91E LYS* 3.5 3.6 + - - -
93E ARG* 6.3 0.4 - - - -
97E LEU* 5.5 7.9 - - + -
112E PHE 4.5 2.2 - - - -
113E GLY* 3.7 14.5 + - - +
114E HIS 3.3 0.8 - - - -
115E GLU* 1.3 110.2 + - + +
117E ASP* 1.3 70.6 + - - +
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Residues in contact with ASP 117 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44E LYS* 6.5 0.2 - - + -
45E SER 4.1 3.1 - - - -
46E ALA* 3.4 10.5 - - - +
47E LYS 3.3 13.0 + - - -
48E THR 3.6 3.8 - - - -
88E VAL* 3.2 6.5 - - - +
89E PHE* 3.1 36.2 + - + +
91E LYS* 3.5 27.4 + - + +
116E PHE* 1.3 82.3 - - - +
118E LEU* 1.3 61.7 + - - +
119E TYR* 3.8 29.1 + - + -
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Residues in contact with LEU 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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43E LYS 3.4 0.5 - - - +
44E LYS* 3.2 5.2 - - - -
45E SER* 2.7 54.3 + - - +
48E THR* 3.6 27.7 + - + +
49E THR 5.0 7.2 - - - +
50E LEU* 5.3 5.2 - - + +
86E ALA* 4.5 7.6 - - + -
87E PHE 3.7 6.1 - - - +
88E VAL* 3.7 20.2 - - + -
99E PHE* 5.1 3.1 - - + -
102E ASN* 6.2 0.2 - - - -
103E SER* 4.4 15.3 - - - +
110E LYS* 6.3 1.1 - - + -
117E ASP* 1.3 72.9 - - - +
119E TYR* 1.3 70.5 + - - +
120E GLU* 4.0 33.4 - - + +
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Residues in contact with TYR 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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39E ILE* 4.0 23.7 - - + +
42E PHE* 3.8 24.2 - + + -
43E LYS 3.6 3.6 - - - -
44E LYS* 4.1 24.9 - - + +
67E ALA* 4.7 17.3 - - + +
86E ALA* 3.5 1.2 - - - -
87E PHE* 3.0 73.0 + + + +
89E PHE* 5.0 1.1 - - + -
117E ASP* 3.8 34.6 + - + -
118E LEU* 1.3 78.4 - - - +
120E GLU* 1.3 62.7 + - - +
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Residues in contact with GLU 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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42E PHE* 3.2 6.7 - - - -
43E LYS* 2.9 49.7 + - - +
45E SER* 4.4 7.8 + - - -
85E LYS 4.5 0.9 - - - +
86E ALA* 3.9 16.4 - - + -
102E ASN* 3.4 8.5 - - + +
103E SER* 2.4 49.3 + - - -
104E MET* 4.4 0.7 - - - +
118E LEU* 4.0 19.2 - - + +
119E TYR* 1.3 75.5 - - - +
121E ASN* 1.3 62.9 + - - +
122E LYS 3.4 0.5 + - - -
125E ILE* 3.6 27.0 - - + +
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Residues in contact with ASN 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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41E GLU 5.1 0.7 - - - -
42E PHE* 3.6 26.8 - - + -
74E CYS* 4.8 3.2 + - - -
75E THR* 5.1 10.1 + - - +
84E CYS 3.9 11.1 + - - +
85E LYS 2.8 27.3 + - - +
102E ASN* 5.3 0.2 + - - -
120E GLU* 1.3 70.3 - - - +
122E LYS* 1.3 66.1 + - - +
123E ASP* 2.9 39.1 + - - +
124E TYR* 3.0 35.8 + - + +
125E ILE* 3.8 7.4 + - - +
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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