Contacts of the helix formed by residues 114 - 131 (chain B) in PDB entry 1GUM
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 114 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112B LEU 3.0 8.8 - - - +
113B LYS* 1.3 94.4 - - + -
115B ASP* 1.3 64.6 + - + +
116B ASP 3.3 0.2 - - - -
117B GLN* 3.3 36.5 - - + +
118B GLN* 3.8 5.5 + - - +
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Residues in contact with ASP 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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113B LYS* 2.4 15.4 + - + +
114B PRO* 1.3 80.2 - - + +
116B ASP* 1.3 73.3 + - - +
117B GLN 3.4 0.2 + - - -
118B GLN* 3.6 10.0 + - - +
119B LYS* 4.1 6.8 + - - +
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Residues in contact with ASP 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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112B LEU* 3.9 7.0 - - + -
113B LYS* 2.3 63.9 + - - +
115B ASP* 1.3 81.1 - - - +
117B GLN* 1.3 63.9 + - - +
118B GLN 3.0 2.2 - - - -
119B LYS* 3.3 8.7 + - + +
120B GLU* 3.0 28.5 + - + +
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Residues in contact with GLN 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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109B HIS* 2.9 59.7 + - + +
110B PRO* 3.7 15.2 + - - +
112B LEU* 3.3 28.9 + - + -
114B PRO* 3.3 33.4 - - + +
115B ASP 3.2 0.6 - - - -
116B ASP* 1.3 79.0 - - - +
118B GLN* 1.3 64.4 + - - +
120B GLU* 3.4 0.9 - - - +
121B VAL* 3.1 15.2 + - - +
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Residues in contact with GLN 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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114B PRO 3.8 4.2 + - - +
115B ASP 3.6 9.2 + - - +
116B ASP 3.0 0.6 - - - -
117B GLN* 1.3 78.8 - - - +
119B LYS* 1.3 66.8 + - - +
120B GLU 3.0 1.8 - - - -
121B VAL* 3.0 37.1 + - - +
122B VAL* 3.3 17.0 + - + +
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Residues in contact with LYS 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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115B ASP 4.1 5.0 + - - +
116B ASP* 3.3 14.0 + - - +
118B GLN* 1.3 75.6 - - - +
120B GLU* 1.3 71.5 + - + +
122B VAL* 3.1 22.9 + - - +
123B ASN* 2.8 64.6 + - - +
126B GLN* 4.1 5.0 + - - -
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Residues in contact with GLU 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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105B LEU* 4.9 12.6 - - - +
108B MET* 5.3 6.6 - - - +
109B HIS* 4.2 7.4 - - + -
112B LEU* 3.6 23.1 - - + -
116B ASP* 3.1 21.8 - - + +
117B GLN 3.4 5.4 - - - +
119B LYS* 1.3 90.3 - - + +
121B VAL* 1.3 64.7 + - - +
123B ASN* 3.1 19.2 + - - +
124B MET* 3.0 28.6 + - + +
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Residues in contact with VAL 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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109B HIS* 3.6 18.2 - - + +
117B GLN 3.1 15.9 - - - +
118B GLN* 3.0 31.8 + - - +
120B GLU* 1.3 73.3 - - - +
122B VAL* 1.3 70.4 - - + +
124B MET* 3.0 14.6 + - + +
125B ALA* 3.0 21.8 + - - +
170B LYS* 4.7 16.4 - - + +
171B ILE* 3.8 26.6 - - + +
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Residues in contact with VAL 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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118B GLN* 3.3 14.5 + - + +
119B LYS* 3.1 20.6 + - - +
121B VAL* 1.3 83.0 - - + +
123B ASN* 1.3 64.7 + - - +
125B ALA* 3.1 9.7 + - + +
126B GLN* 3.0 41.8 + - + +
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Residues in contact with ASN 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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105B LEU* 4.5 9.1 - - - +
119B LYS* 2.8 32.1 + - - +
120B GLU* 3.1 23.3 + - - +
121B VAL 3.1 0.4 - - - -
122B VAL* 1.3 78.9 - - - +
124B MET* 1.3 62.2 + - - +
126B GLN* 3.0 12.5 + - - +
127B LYS* 2.9 53.8 + - - +
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Residues in contact with MET 124 (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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102B LEU* 4.2 3.0 - - + +
105B LEU* 3.5 51.1 - - + +
106B LEU* 3.7 30.3 - - + -
109B HIS* 3.7 26.7 - - + -
120B GLU* 3.0 17.7 + - + +
121B VAL* 3.3 12.8 - - - +
123B ASN* 1.3 72.5 - - - +
125B ALA* 1.3 56.7 + - - +
127B LYS* 3.1 2.3 + - - +
128B ALA* 2.7 38.0 + - - +
167B LEU* 3.8 22.7 - - + -
170B LYS* 4.6 10.8 - - + -
171B ILE* 4.4 6.1 - - + -
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Residues in contact with ALA 125 (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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121B VAL 3.0 8.1 + - - +
122B VAL* 3.2 13.9 - - + +
124B MET* 1.3 80.8 - - - +
126B GLN* 1.3 65.0 + - + +
128B ALA* 3.3 1.0 + - - +
129B ILE* 3.0 32.1 + - + +
171B ILE* 3.7 18.8 - - + -
174B ILE* 3.7 17.9 - - + -
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Residues in contact with GLN 126 (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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119B LYS* 4.1 9.7 + - - -
122B VAL* 3.0 33.3 + - + +
123B ASN* 3.0 13.7 + - - +
125B ALA* 1.3 79.9 - - + +
127B LYS* 1.3 61.9 + - - +
129B ILE* 4.4 3.4 - - - -
130B ILE* 2.7 53.3 + - + +
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Residues in contact with LYS 127 (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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102B LEU* 4.1 13.5 - - + -
105B LEU* 4.4 9.2 - - + -
123B ASN* 2.9 50.5 + - - +
124B MET 3.7 3.6 - - - +
126B GLN* 1.3 77.4 - - - +
128B ALA* 1.3 60.3 + - - +
130B ILE* 4.8 6.0 - - - +
131B ARG* 2.7 74.4 + - - +
132B TYR* 3.3 11.5 + - + -
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Residues in contact with ALA 128 (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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102B LEU* 4.1 20.4 - - + +
124B MET 2.7 21.7 + - - +
125B ALA 3.6 3.6 - - - +
127B LYS* 1.3 76.4 - - - +
129B ILE* 1.3 63.3 + - - +
132B TYR* 3.3 2.8 + - - -
133B PHE* 2.8 58.2 + - + +
167B LEU* 4.4 5.6 - - + -
174B ILE* 4.3 9.4 - - + -
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Residues in contact with ILE 129 (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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125B ALA* 3.0 25.0 + - + +
126B GLN* 3.7 3.8 - - - +
128B ALA* 1.3 81.1 - - - +
130B ILE* 1.3 69.6 + - + +
133B PHE* 4.5 1.3 - - + -
134B PRO* 3.0 19.9 - - - +
174B ILE* 3.6 27.6 - - + +
176B SER* 5.9 0.9 - - - +
177B ALA* 5.9 1.3 - - + -
178B PHE* 3.5 35.4 - - + -
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Residues in contact with ILE 130 (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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53A GLN* 5.4 8.1 + - + +
126B GLN* 2.7 38.1 + - + +
127B LYS* 4.8 6.1 - - - +
129B ILE* 1.3 92.2 - - + +
131B ARG* 1.3 66.8 + - + +
134B PRO* 3.5 11.7 - - - +
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Residues in contact with ARG 131 (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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45A GLN* 5.3 2.6 - - - +
51A LEU 4.8 0.2 - - - +
52A PHE* 3.1 30.8 + - + +
53A GLN* 3.6 33.6 + - + +
54A GLN* 3.5 28.2 - - - +
127B LYS* 2.7 55.2 + - - +
130B ILE* 1.3 81.0 - - + +
132B TYR* 1.3 80.0 + - + +
134B PRO* 4.2 1.2 - - - +
135B VAL* 3.4 20.8 - - - +
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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