Contacts of the helix formed by residues 120 - 140 (chain A) in PDB entry 1OCU
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 SER 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A SER 4.5 0.4 + - - -
117A ASN* 2.7 35.1 + - - +
119A PHE* 1.3 74.1 - - - +
121A ASN* 1.3 65.8 + - - +
122A GLU* 4.2 4.1 + - - +
123A VAL* 2.9 20.6 + - - +
124A ILE* 3.1 24.5 + - - +
52B ASP* 4.1 0.4 - - - -
53B SER* 4.6 2.9 - - - +
54B LYS 6.1 0.7 - - - +
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Residues in contact with ASN 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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120A SER* 1.3 71.3 - - - +
122A GLU* 1.3 81.3 + - - +
124A ILE* 3.0 7.6 + - - +
125A GLU* 2.9 27.6 + - - +
52B ASP* 3.5 32.9 - - - +
54B LYS* 6.0 4.7 - - + +
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Residues in contact with GLU 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A SER* 3.6 4.7 + - - +
121A ASN* 1.3 87.0 - - - +
123A VAL* 1.3 58.1 + - + +
125A GLU* 3.4 6.3 + - + +
126A GLU* 3.0 31.3 + - + +
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Residues in contact with VAL 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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113A ILE* 4.1 23.1 - - + -
117A ASN* 3.2 39.5 - - + +
118A ARG* 4.1 16.8 - - - +
120A SER* 2.9 20.0 - - - +
121A ASN 3.1 0.8 - - - -
122A GLU* 1.3 76.8 - - + +
124A ILE* 1.3 65.0 + - + +
126A GLU* 3.5 4.3 + - - +
127A ARG* 3.1 28.0 + - + +
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Residues in contact with ILE 124 (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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43A PRO* 3.5 35.7 - - + -
45A THR* 4.8 0.7 - - - +
58A THR* 3.5 29.6 - - + +
60A TYR* 3.9 15.7 - - - +
118A ARG 3.4 23.8 - - - +
119A PHE* 4.3 8.5 - - - +
120A SER 3.1 18.7 + - - +
121A ASN* 3.0 7.6 + - - +
123A VAL* 1.3 76.1 - - + +
125A GLU* 1.3 58.4 - - - +
127A ARG* 3.8 3.6 - - - +
128A ARG* 2.9 28.3 + - - +
51B MET* 4.7 7.0 - - + +
52B ASP* 4.6 9.2 - - + -
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Residues in contact with GLU 125 (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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43A PRO* 5.6 2.5 - - - +
121A ASN* 2.9 21.8 + - - +
122A GLU* 3.7 10.1 - - + +
124A ILE* 1.3 75.8 - - - +
126A GLU* 1.3 67.1 + - - +
128A ARG* 3.1 40.1 + - - +
129A GLN* 3.0 34.3 + - + +
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Residues in contact with GLU 126 (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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110A PRO* 5.6 0.3 - - - +
122A GLU* 3.0 19.0 + - + +
123A VAL* 4.1 4.5 - - - +
125A GLU* 1.3 74.1 - - - +
127A ARG* 1.3 61.6 + - - +
129A GLN* 3.3 12.3 + - + +
130A GLY* 2.9 25.6 + - - -
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Residues in contact with ARG 127 (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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58A THR* 6.3 0.6 - - - -
60A TYR* 3.2 26.2 + - - +
82A TYR* 3.3 37.8 - - + +
110A PRO* 4.4 10.5 - - + +
111A GLY 3.0 26.1 + - - -
112A LYS* 4.0 0.4 - - - +
113A ILE* 3.3 17.1 - - + +
118A ARG* 5.0 7.7 + - - +
123A VAL* 3.1 22.4 + - + +
124A ILE* 3.9 4.6 - - - +
126A GLU* 1.3 74.4 - - - +
128A ARG* 1.3 60.8 + - - +
130A GLY* 3.1 2.5 + - - +
131A LEU* 2.8 42.6 + - + +
1163A PIB 2.9 46.7 + - - -
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Residues in contact with ARG 128 (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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39A GLU* 4.6 4.8 + - - -
40A VAL* 2.9 30.4 + - + +
41A HIS* 3.7 24.4 - - - +
43A PRO* 3.8 18.2 - - + -
60A TYR* 4.0 23.5 - - + -
124A ILE 2.9 19.6 + - - +
125A GLU* 3.1 38.4 + - - +
127A ARG* 1.3 76.9 - - - +
129A GLN* 1.3 79.1 + - - +
131A LEU* 3.1 5.5 + - - +
132A ASN* 2.8 39.9 + - - +
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Residues in contact with GLN 129 (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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125A GLU* 3.0 26.6 + - - +
126A GLU* 3.6 13.8 - - + +
128A ARG* 1.3 98.9 - - - +
130A GLY* 1.3 63.4 + - - +
132A ASN* 3.3 7.7 + - - +
133A THR* 3.1 28.8 + - - +
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Residues in contact with GLY 130 (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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110A PRO* 4.2 21.0 - - - +
126A GLU 2.9 14.6 + - - -
127A ARG 3.1 3.8 + - - -
129A GLN* 1.3 77.5 - - - +
131A LEU* 1.3 56.6 + - - +
133A THR* 3.5 5.2 + - - -
134A TRP* 2.9 30.0 + - - +
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Residues in contact with LEU 131 (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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40A VAL* 3.8 12.1 - - + +
60A TYR* 3.8 39.9 - - + -
82A TYR* 4.2 10.1 - - + -
85A PHE* 3.8 43.1 - - + -
109A LEU* 4.0 11.2 - - + -
110A PRO* 4.0 16.8 - - + +
127A ARG* 2.8 32.1 + - + +
128A ARG 3.6 3.8 - - - +
130A GLY* 1.3 68.6 - - - +
132A ASN* 1.3 61.6 + - - +
134A TRP* 3.7 4.0 - - - +
135A MET* 2.9 33.1 + - - +
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Residues in contact with ASN 132 (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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39A GLU* 3.1 19.8 - - - +
40A VAL* 2.8 43.8 + - - +
128A ARG* 2.8 23.4 + - - +
129A GLN* 3.6 7.4 + - - +
130A GLY 3.3 0.2 - - - -
131A LEU* 1.3 77.5 - - - +
133A THR* 1.3 65.9 + - - +
135A MET* 3.7 1.4 - - - +
136A GLN* 3.0 49.1 + - - +
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Residues in contact with THR 133 (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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129A GLN* 3.1 16.3 + - - +
130A GLY* 3.8 5.2 - - - -
132A ASN* 1.3 81.0 + - - +
134A TRP* 1.3 65.1 + - - +
136A GLN* 3.5 9.4 + - - +
137A SER* 3.1 25.0 + - - -
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Residues in contact with TRP 134 (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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85A PHE* 4.2 16.4 - + - -
88A PHE* 3.8 38.6 - + - -
89A ARG* 4.2 15.3 - - + -
92A LEU* 4.9 1.3 - - + -
106A VAL* 3.9 14.6 - - + -
107A PRO* 2.7 36.5 + - + +
108A HIS 3.4 23.5 + - - -
109A LEU* 3.4 33.4 - - + -
110A PRO* 4.6 2.2 - - + -
130A GLY 2.9 19.1 + - - +
131A LEU* 3.7 6.7 - - + +
133A THR* 1.3 78.6 - - - +
135A MET* 1.3 67.7 + - + +
137A SER* 3.3 5.5 + - - -
138A VAL* 3.0 49.0 + - + +
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Residues in contact with MET 135 (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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38A ILE* 3.6 28.0 - - + -
40A VAL* 3.8 19.5 - - + -
62A ILE* 4.5 5.2 - - + -
85A PHE* 4.4 6.1 - - + -
88A PHE* 4.4 9.4 - - + -
131A LEU 2.9 18.4 + - - +
132A ASN 3.7 3.4 - - - +
134A TRP* 1.3 89.0 - - + +
136A GLN* 1.3 60.8 + - + +
138A VAL* 4.4 2.7 - - + -
139A ALA* 2.9 43.8 + - + +
151A LEU* 3.7 29.4 - - + -
154A PHE* 3.9 25.1 - - + -
155A ILE* 4.4 6.3 - - + -
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Residues in contact with GLN 136 (chain A).
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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38A ILE* 2.8 41.8 + - + +
39A GLU* 4.3 4.4 - - - +
132A ASN* 3.0 42.6 + - - +
133A THR* 4.0 7.8 - - - +
135A MET* 1.3 76.6 - - + +
137A SER* 1.3 57.4 + - - +
139A ALA 3.9 0.2 - - - -
140A GLY* 3.0 26.5 + - - -
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Residues in contact with SER 137 (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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107A PRO* 4.2 18.3 - - - +
133A THR* 3.1 20.2 + - - -
134A TRP* 3.6 6.3 - - - -
135A MET 3.2 0.2 - - - -
136A GLN* 1.3 75.6 - - - +
138A VAL* 1.3 65.0 + - - +
140A GLY* 3.4 8.1 + - - -
141A HIS* 3.6 12.0 + - - +
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Residues in contact with VAL 138 (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 PHE* 4.5 4.0 - - + -
92A LEU* 3.7 23.8 - - + -
106A VAL* 4.2 14.1 - - + -
107A PRO* 4.4 10.1 - - + -
134A TRP* 3.0 48.8 + - + +
135A MET* 3.9 9.4 - - + +
137A SER* 1.3 75.9 - - - +
139A ALA* 1.3 61.9 + - - +
140A GLY 3.3 1.0 + - - -
141A HIS* 3.3 10.9 + - - +
144A LEU* 3.4 27.4 - - + +
151A LEU* 3.9 16.6 - - + -
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Residues in contact with ALA 139 (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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36A LEU* 4.0 26.9 - - + +
38A ILE* 4.1 11.4 - - + -
135A MET* 2.9 36.3 + - + +
136A GLN 3.9 0.2 - - - -
138A VAL* 1.3 73.6 - - - +
140A GLY* 1.3 56.4 + - - +
141A HIS 3.2 1.3 - - - -
144A LEU* 5.7 0.2 - - - -
145A GLN* 2.8 29.4 + - - +
151A LEU* 4.1 16.5 - - + +
155A ILE* 4.4 3.6 - - + -
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Residues in contact with GLY 140 (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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36A LEU* 5.6 2.7 - - - -
136A GLN 3.0 19.4 + - - -
137A SER 3.4 3.8 + - - -
138A VAL 3.1 1.0 - - - -
139A ALA* 1.3 76.8 - - - +
141A HIS* 1.3 61.0 + - - +
142A PRO* 3.4 9.5 - - - +
145A GLN* 3.6 13.1 + - - +
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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