Contacts of the helix formed by residues 110 - 123 (chain A) in PDB entry 1W31
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 GLY 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A ASP* 5.8 0.9 - - - -
104A ALA 5.2 2.7 - - - -
107A ASP* 2.7 28.2 + - - -
109A ALA* 1.3 79.9 - - - +
111A PRO* 1.3 71.6 - - - +
112A VAL 3.4 1.8 - - - -
113A ILE 3.8 1.2 + - - -
114A GLN* 3.0 32.3 + - - +
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Residues in contact with PRO 111 (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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47A ILE* 3.3 50.7 - - + +
48A SER 3.8 8.3 - - - +
49A ASP* 4.1 22.8 - - + +
68A VAL* 5.6 1.1 - - + -
90A GLY* 4.3 3.4 - - - -
91A VAL 3.9 11.7 - - - +
92A PRO* 4.2 15.3 - - + -
104A ALA 5.7 1.3 - - - +
110A GLY* 1.3 80.8 - - - +
112A VAL* 1.3 56.8 + - - +
114A GLN* 3.6 5.0 - - + +
115A GLY* 2.7 33.6 + - - -
137A TYR* 5.3 6.5 - - + +
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Residues in contact with VAL 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ILE* 5.2 1.8 - - - -
88A LEU* 3.9 13.1 - - + +
89A PHE* 4.2 5.2 - - - +
90A GLY* 3.4 22.2 - - - +
105A ALA 5.0 2.2 - - - +
110A GLY 3.4 1.2 - - - -
111A PRO* 1.3 75.7 - - - +
113A ILE* 1.3 64.8 + - - +
115A GLY* 3.0 3.8 + - - -
116A ILE* 2.9 24.5 + - + +
130A CYS* 3.9 25.6 - - + -
131A ASP 5.9 1.3 - - - +
137A TYR* 3.3 25.6 - - - +
168A TYR* 3.6 33.9 - - + +
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Residues in contact with ILE 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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105A ALA 5.4 0.7 - - - +
106A ASP* 3.3 36.8 - - + +
107A ASP 3.8 8.1 - - - +
108A PRO* 3.6 28.9 - - + +
110A GLY 3.8 2.4 + - - -
112A VAL* 1.3 78.4 - - - +
114A GLN* 1.3 61.2 + - - +
116A ILE* 3.4 6.9 + - - +
117A LYS* 3.0 35.1 + - + +
167A ASN* 4.5 7.6 - - + +
168A TYR* 4.0 24.5 - - + -
171A ALA* 3.7 27.1 - - + -
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Residues in contact with GLN 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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68A VAL* 4.1 22.3 - - + +
108A PRO 2.9 23.4 + - - -
109A ALA* 3.7 15.8 - - - +
110A GLY 3.0 25.3 + - - +
111A PRO* 3.6 4.3 - - + +
113A ILE* 1.3 80.3 + - - +
115A GLY* 1.3 59.3 + - - +
117A LYS* 3.5 12.0 + - - +
118A PHE* 3.0 28.3 + - - +
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Residues in contact with GLY 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ILE* 5.0 3.1 - - - -
68A VAL* 4.7 4.0 - - - +
71A LEU* 4.5 14.1 - - - -
88A LEU* 4.0 12.8 - - - -
111A PRO 2.7 19.2 + - - -
112A VAL 3.5 3.8 - - - -
114A GLN* 1.3 72.6 - - - +
116A ILE* 1.3 58.4 + - - +
118A PHE* 3.5 5.6 - - - +
119A ILE* 2.8 35.5 + - - +
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Residues in contact with ILE 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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88A LEU* 4.1 6.5 - - + -
112A VAL* 2.9 24.1 + - + +
113A ILE* 3.6 15.9 - - + +
115A GLY* 1.3 76.9 - - - +
117A LYS* 1.3 58.9 + - - +
119A ILE* 3.7 0.5 - - - -
120A ARG* 2.8 42.0 + - + +
128A ILE* 3.9 13.6 - - + +
130A CYS* 3.5 33.2 - - - -
168A TYR* 3.9 22.4 - - - +
171A ALA* 3.8 17.7 - - + +
172A GLY 3.7 27.8 - - - -
173A ALA* 4.0 2.7 - - + -
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Residues in contact with LYS 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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113A ILE* 3.0 27.2 + - + +
114A GLN* 3.8 13.9 - - - +
116A ILE* 1.3 76.9 - - + +
118A PHE* 1.3 61.5 + - - +
120A ARG* 3.7 6.3 + - - +
121A GLU* 3.4 23.4 + - - +
170A LYS 5.3 1.2 + - - -
171A ALA* 3.3 37.6 + - - +
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Residues in contact with PHE 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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68A VAL* 3.5 37.0 - - + -
71A LEU* 3.8 17.9 - - + -
72A LYS* 3.4 36.8 - - + -
75A LEU* 4.9 0.2 - - + -
114A GLN 3.0 18.6 + - - +
115A GLY* 3.5 5.8 - - - +
117A LYS* 1.3 77.8 - - - +
119A ILE* 1.3 69.7 + - + +
121A GLU* 3.4 2.7 + - - -
122A TYR* 3.1 55.4 + + + +
123A PHE* 3.6 24.2 - + - -
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Residues in contact with ILE 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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45A LEU* 4.4 3.1 - - + -
71A LEU* 4.6 5.2 - - + -
75A LEU* 4.0 22.4 - - + -
86A VAL* 4.1 22.4 - - + -
88A LEU* 4.2 21.5 - - + -
115A GLY 2.8 23.9 + - - +
118A PHE* 1.3 81.6 - - + +
120A ARG* 1.3 60.0 + - - +
123A PHE* 2.7 52.2 + - + +
126A LEU* 4.1 16.2 - - + -
128A ILE* 3.4 28.5 - - + -
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Residues in contact with ARG 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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116A ILE* 2.8 37.8 + - + +
117A LYS* 4.0 6.7 - - - +
118A PHE 3.4 0.2 - - - -
119A ILE* 1.3 76.5 - - - +
121A GLU* 1.3 58.6 + - - +
123A PHE 4.6 1.4 + - - -
124A PRO* 3.5 59.7 + - - +
128A ILE* 3.2 22.2 - - + -
171A ALA 5.3 0.9 - - - +
172A GLY* 3.6 22.9 + - - +
174A HIS* 3.7 24.9 + - - -
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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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117A LYS 3.4 14.5 + - - +
118A PHE* 3.4 3.9 + - - +
119A ILE 3.1 0.4 - - - -
120A ARG* 1.3 81.4 - - - +
122A TYR* 1.3 95.4 + - + +
123A PHE 3.5 0.2 - - - -
124A PRO* 4.1 7.6 - - - +
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Residues in contact with TYR 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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72A LYS* 4.8 22.9 - - + -
76A LYS* 5.9 1.0 + - - -
118A PHE* 3.1 49.9 + + + +
121A GLU* 1.3 101.8 + - + +
123A PHE* 1.3 88.7 + - + +
124A PRO* 3.6 6.1 - - - +
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Residues in contact with PHE 123 (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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72A LYS* 3.9 25.4 - - + -
75A LEU* 3.6 37.2 - - + -
76A LYS* 4.1 30.1 - - - -
79A VAL* 4.0 24.2 - - + -
118A PHE* 3.6 27.4 - + - -
119A ILE* 2.7 29.5 + - + +
120A ARG* 4.6 0.7 + - - -
122A TYR* 1.3 85.9 - - + +
124A PRO* 1.3 59.1 - - - +
125A GLU* 2.8 11.4 + - - +
126A LEU* 3.0 31.4 + - + +
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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