Contacts of the helix formed by residues 114 - 131 (chain H) in PDB entry 1GUL
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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112H LEU 3.3 7.6 - - - +
113H LYS* 1.3 93.9 - - + -
115H ASP* 1.3 63.0 + - + +
116H ASP 3.3 0.2 - - - -
117H GLN* 3.3 32.4 + - - +
118H GLN* 3.9 5.2 + - - +
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Residues in contact with ASP 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113H LYS* 2.6 10.5 + - + +
114H PRO* 1.3 79.5 - - + +
116H ASP* 1.3 74.8 + - - +
117H GLN 3.2 0.9 + - - -
118H GLN* 3.5 11.6 + - - +
119H LYS* 4.0 5.7 + - - +
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Residues in contact with ASP 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112H LEU* 4.1 9.4 - - + -
113H LYS* 2.3 59.3 + - - +
115H ASP* 1.3 81.1 - - - +
117H GLN* 1.3 64.3 + - - -
118H GLN 3.1 2.2 - - - -
119H LYS* 3.4 9.5 + - + +
120H GLU* 2.8 31.8 + - + +
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Residues in contact with GLN 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109H HIS* 2.8 58.7 + - + +
110H PRO* 3.6 20.0 + - - +
112H LEU* 3.3 26.3 + - + -
113H LYS 3.1 0.6 + - - -
114H PRO* 3.4 30.5 - - + +
115H ASP 3.1 0.8 - - - -
116H ASP* 1.3 78.6 - - - +
118H GLN* 1.3 64.8 + - - +
120H GLU* 3.1 8.7 - - - +
121H VAL* 3.2 6.1 + - - +
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Residues in contact with GLN 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109H HIS* 5.7 0.7 - - - -
114H PRO 3.9 4.2 + - - +
115H ASP 3.5 9.2 + - - +
116H ASP 3.1 0.6 - - - -
117H GLN* 1.3 79.5 - - - +
119H LYS* 1.3 67.0 + - - +
120H GLU 3.0 2.3 + - - -
121H VAL* 3.1 36.1 + - - +
122H VAL* 3.3 18.1 + - + +
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Residues in contact with LYS 119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115H ASP 4.0 3.7 + - - +
116H ASP* 3.4 14.5 + - - +
118H GLN* 1.3 75.4 - - - +
120H GLU* 1.3 66.8 + - + +
122H VAL* 3.1 18.4 + - + +
123H ASN* 2.8 67.0 + - - +
126H GLN* 4.3 7.0 + - - -
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Residues in contact with GLU 120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105H LEU* 5.0 11.4 - - - +
108H MET* 5.4 6.7 - - - +
109H HIS* 3.9 8.5 - - + -
112H LEU* 3.4 25.5 - - + +
116H ASP* 2.8 23.1 - - + +
117H GLN 3.1 7.0 - - - +
119H LYS* 1.3 88.1 + - + +
121H VAL* 1.3 61.3 + - - +
123H ASN* 3.1 16.3 + - - +
124H MET* 2.9 35.3 + - + +
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Residues in contact with VAL 121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109H HIS* 3.7 17.9 - - + +
117H GLN 3.2 14.1 + - - +
118H GLN* 3.1 30.6 + - - +
120H GLU* 1.3 74.5 - - - +
122H VAL* 1.3 70.1 + - + +
124H MET* 3.1 10.8 + - + +
125H ALA* 2.9 21.7 + - + +
170H LYS* 4.4 21.1 - - + +
171H ILE* 3.8 25.9 - - + +
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Residues in contact with VAL 122 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118H GLN* 3.7 16.4 - - + +
119H LYS* 3.1 19.9 + - + +
121H VAL* 1.3 83.7 - - + +
123H ASN* 1.3 63.8 + - - +
125H ALA* 3.0 10.3 + - + +
126H GLN* 2.9 41.3 + - + +
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Residues in contact with ASN 123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105H LEU* 4.1 14.3 - - - +
119H LYS* 2.8 30.7 + - - +
120H GLU* 3.5 21.0 + - - +
121H VAL 3.1 0.4 - - - -
122H VAL* 1.3 78.7 - - - +
124H MET* 1.3 62.7 + - - +
126H GLN* 3.0 12.2 + - - +
127H LYS* 2.8 54.6 + - - +
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Residues in contact with MET 124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102H LEU* 4.4 2.4 - - + +
105H LEU* 3.8 43.7 - - + +
106H LEU* 3.8 29.6 - - + -
109H HIS* 3.6 33.7 - - + +
120H GLU* 2.9 19.2 + - + +
121H VAL* 3.5 13.9 - - - +
123H ASN* 1.3 72.8 - - - +
125H ALA* 1.3 65.3 - - - +
127H LYS* 3.2 1.2 + - - +
128H ALA* 2.8 27.4 + - - +
167H LEU* 3.9 21.5 - - + -
170H LYS* 4.5 11.4 - - + -
171H ILE* 4.5 4.0 - - + -
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Residues in contact with ALA 125 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121H VAL 2.9 10.1 + - - +
122H VAL* 3.2 12.6 - - + +
124H MET* 1.3 81.6 - - - +
126H GLN* 1.3 65.9 + - + +
128H ALA* 3.2 0.5 + - - +
129H ILE* 2.9 33.6 + - + +
171H ILE* 3.7 24.9 - - + +
174H ILE* 4.1 8.7 - - + -
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Residues in contact with GLN 126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119H LYS* 4.3 12.0 + - - -
122H VAL* 2.9 35.1 + - + +
123H ASN* 3.0 13.1 + - - +
125H ALA* 1.3 80.0 - - + +
127H LYS* 1.3 60.3 + - - +
129H ILE* 4.5 4.5 - - - -
130H ILE* 2.8 54.2 + - + +
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Residues in contact with LYS 127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102H LEU* 4.2 13.9 - - + -
105H LEU* 4.2 8.7 - - + -
123H ASN* 2.8 50.2 + - - +
124H MET* 3.7 3.8 - - - +
126H GLN* 1.3 75.7 - - - +
128H ALA* 1.3 59.3 + - - +
130H ILE* 4.8 4.4 - - - +
131H ARG* 2.6 67.9 + - - +
132H TYR* 3.2 14.8 + - + +
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Residues in contact with ALA 128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102H LEU* 4.2 14.1 - - + +
124H MET 2.8 17.4 + - - +
125H ALA 3.5 3.4 - - - +
127H LYS* 1.3 80.8 - - - +
129H ILE* 1.3 60.9 + - - +
132H TYR* 3.3 1.6 + - - -
133H PHE* 2.8 50.2 + - + +
167H LEU* 4.3 9.9 - - + -
174H ILE* 3.9 20.4 - - + -
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Residues in contact with ILE 129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125H ALA* 2.9 25.2 + - + +
126H GLN* 3.7 5.2 - - - +
128H ALA* 1.3 83.0 - - + +
130H ILE* 1.3 66.8 + - + +
133H PHE* 4.4 0.9 - - + -
134H PRO* 2.9 22.2 - - - +
174H ILE* 3.8 36.3 - - + +
177H ALA* 6.2 0.9 - - + -
178H PHE* 3.7 23.2 - - + -
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Residues in contact with ILE 130 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53G GLN* 5.4 4.7 - - + +
126H GLN* 2.8 37.6 + - + +
127H LYS* 4.8 4.9 - - - +
129H ILE* 1.3 92.5 - - + +
131H ARG* 1.3 73.8 + - + +
132H TYR 3.7 0.2 - - - -
134H PRO* 3.7 12.4 - - - +
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Residues in contact with ARG 131 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45G GLN* 4.5 3.6 - - - +
52G PHE* 3.3 28.7 - - - +
53G GLN* 3.6 29.7 - - - +
54G GLN* 4.2 12.4 - - - +
301G IBG 2.8 38.4 + - - -
127H LYS* 2.6 50.1 + - - +
130H ILE* 1.3 85.5 - - + +
132H TYR* 1.3 84.3 + - + +
134H PRO* 4.5 0.9 - - - -
135H VAL* 3.6 19.1 - - - +
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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