Contacts of the helix formed by residues 116 - 134 (chain A) in PDB entry 3RC3
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 ASP 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A THR* 2.6 36.7 + - + +
111A ALA* 5.2 4.7 - - - +
114A GLY 3.3 5.6 + - - +
115A LEU* 1.3 74.9 - - - +
117A ALA* 1.3 57.6 + - - +
118A ARG* 3.4 8.1 + - - +
119A LEU* 3.1 23.9 + - - +
120A PHE* 2.8 30.9 + - - +
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Residues in contact with ALA 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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116A ASP* 1.3 75.9 - - - +
118A ARG* 1.3 58.2 + - - +
120A PHE* 3.9 4.8 - - - +
121A HIS* 3.0 30.0 + - - +
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Residues in contact with ARG 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A THR* 3.3 25.7 + - - +
62A SER* 3.6 45.6 + - - +
64A PHE 4.9 5.9 + - - -
66A PRO* 6.3 0.4 - - - +
116A ASP* 3.5 12.5 - - - +
117A ALA* 1.3 77.0 - - - +
119A LEU* 1.3 64.4 + - + +
121A HIS* 3.4 4.4 + - - +
122A GLN* 2.9 53.9 + - + +
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Residues in contact with LEU 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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61A THR* 3.7 33.7 - - + +
64A PHE* 3.7 27.8 - - + +
114A GLY 3.4 22.0 - - - +
115A LEU* 3.6 17.7 - - + -
116A ASP* 3.1 11.9 + - - +
118A ARG* 1.3 76.8 - - + +
120A PHE* 1.3 59.3 + - - +
122A GLN* 4.3 5.6 - - - +
123A ALA* 2.7 39.0 + - - +
170A PHE* 3.6 35.6 - - + -
173A LEU* 4.0 12.1 - - + -
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Residues in contact with PHE 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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100A PHE* 4.6 2.9 - + - -
101A TYR* 3.6 49.8 - + - -
106A ILE* 3.6 34.5 - - + -
107A GLN* 3.7 28.9 - - + -
110A GLY* 4.3 12.8 - - - -
115A LEU* 3.8 13.9 - - + +
116A ASP 2.8 19.3 + - - +
117A ALA* 3.9 5.4 - - - +
119A LEU* 1.3 76.4 - - - +
121A HIS* 1.3 67.4 + - + +
124A PHE* 2.9 27.0 + - + +
162A PHE* 3.7 32.7 - + - -
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Residues in contact with HIS 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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101A TYR* 2.7 39.5 + + - +
117A ALA 3.0 20.4 + - - +
118A ARG* 3.6 5.2 - - - +
120A PHE* 1.3 79.2 - - + +
122A GLN* 1.3 71.4 + - + +
124A PHE* 3.2 2.4 + - - +
125A ILE* 3.1 55.2 + - + +
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Residues in contact with GLN 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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64A PHE 4.9 1.4 - - - +
66A PRO* 3.6 27.6 - - + +
118A ARG* 2.9 44.3 + - + +
119A LEU* 4.3 4.2 - - - +
121A HIS* 1.3 83.5 - - + +
123A ALA* 1.3 66.1 + - - +
125A ILE* 3.5 6.5 + - - +
126A SER* 3.4 21.7 + - - -
169A ILE* 5.1 2.5 - - + +
170A PHE* 3.6 30.0 - - + -
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Residues in contact with ALA 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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115A LEU* 4.7 1.1 - - + -
119A LEU 2.7 22.1 + - - +
120A PHE 3.8 0.9 - - - +
122A GLN* 1.3 75.2 - - - +
124A PHE* 1.3 58.3 + - - +
126A SER* 3.5 0.7 + - - -
127A PHE* 2.8 30.7 + - - +
162A PHE* 3.7 13.7 - - + -
165A HIS* 3.8 4.4 - - + -
166A ALA* 3.7 34.8 - - + -
169A ILE* 4.4 11.9 - - + -
170A PHE* 4.1 6.0 - - + -
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Residues in contact with PHE 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LEU* 3.1 51.1 - - + -
98A ASP* 4.0 5.8 - - - -
100A PHE* 4.1 20.2 - + - -
101A TYR* 3.4 44.4 - + + -
120A PHE* 2.9 19.2 + + + +
121A HIS 3.2 3.1 + - - +
123A ALA* 1.3 78.1 - - - +
125A ILE* 1.3 67.5 + - + +
127A PHE* 3.1 5.5 + + - +
128A ARG* 2.8 60.7 + - + +
162A PHE* 3.6 13.0 - + + -
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Residues in contact with ILE 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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121A HIS* 3.1 53.2 + - + +
122A GLN* 3.9 6.5 - - - +
123A ALA 3.3 0.2 - - - -
124A PHE* 1.3 86.1 - - + +
126A SER* 1.3 59.2 + - - +
128A ARG* 3.8 28.2 + - - +
129A ASN* 3.0 32.8 + - + +
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Residues in contact with SER 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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69A VAL* 4.4 12.0 + - - +
122A GLN 3.4 13.9 + - - -
123A ALA 3.8 1.6 - - - -
125A ILE* 1.3 79.4 - - - +
127A PHE* 1.3 61.5 + - - +
129A ASN* 3.3 7.2 - - - +
130A TYR* 2.7 30.7 + - - +
165A HIS* 2.9 18.3 + - - -
169A ILE* 3.4 19.3 - - - +
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Residues in contact with PHE 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LEU* 4.4 7.4 - - + -
100A PHE* 5.0 3.4 - + - -
123A ALA 2.8 19.6 + - - +
124A PHE* 3.5 11.0 - + - +
126A SER* 1.3 76.6 - - - +
128A ARG* 1.3 63.6 + - - +
130A TYR* 3.2 6.3 + + + +
131A ILE* 3.0 54.7 + - + +
141A ILE* 4.0 19.5 - - + -
158A LEU* 4.0 23.1 - - + -
161A PHE* 4.0 6.5 - - + -
162A PHE* 3.7 52.0 - + + -
165A HIS* 3.4 32.5 + + + -
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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
----------------------------------------------------------
94A LYS* 4.1 20.9 - - - +
97A LEU* 3.5 29.4 - - + -
98A ASP* 2.9 38.0 + - - -
124A PHE* 2.8 38.4 + - + +
125A ILE* 3.8 29.3 + - - +
127A PHE* 1.3 75.7 - - - +
129A ASN* 1.3 58.2 + - - +
131A ILE* 3.3 2.3 + - - +
132A MSE 2.8 44.8 + - + +
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Residues in contact with ASN 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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71A PRO* 4.2 12.0 - - - +
125A ILE* 3.0 23.1 + - + +
126A SER* 3.3 11.0 - - - +
128A ARG* 1.3 77.8 - - - +
130A TYR* 1.3 63.0 + - - +
132A MSE 4.7 2.9 - - - -
133A GLN* 2.5 60.6 + - - +
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Residues in contact with TYR 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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69A VAL* 3.9 23.3 + - + +
70A LYS 3.3 29.2 - - - -
71A PRO* 3.8 11.9 - - + -
72A GLN* 2.9 44.0 + - + +
126A SER 2.7 21.1 + - - +
127A PHE* 3.5 7.4 - + - +
129A ASN* 1.3 74.0 - - - +
131A ILE* 1.3 66.7 + - + +
134A SER* 2.7 41.7 + - - -
137A LEU* 3.9 19.5 - - + -
138A ASP* 5.5 2.1 + - - -
141A ILE* 6.1 3.6 - - + -
165A HIS* 3.9 17.3 - + + +
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Residues in contact with ILE 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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88A LEU* 5.3 2.1 - - + +
90A LYS* 4.0 11.3 + - - -
93A VAL* 3.7 28.5 - - + -
97A LEU* 3.9 19.7 - - + -
127A PHE* 3.0 58.3 + - + +
128A ARG 3.7 3.4 - - - +
130A TYR* 1.3 80.6 - - + +
132A MSE 1.3 61.5 + - - +
133A GLN 3.5 0.2 + - - -
134A SER 4.1 4.5 + - - +
137A LEU* 4.2 22.8 - - + +
141A ILE* 4.3 14.8 - - + -
145A LEU* 3.9 22.2 - - + -
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Residues in contact with MSE 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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90A LYS* 3.2 70.1 + - + +
91A ASN* 5.5 1.1 - - - +
93A VAL* 3.9 22.9 - - - -
94A LYS* 4.1 23.3 - - + -
97A LEU* 4.4 1.8 - - + -
128A ARG* 2.8 40.7 + - + +
129A ASN* 4.1 4.0 - - - +
131A ILE* 1.3 74.3 - - - +
133A GLN* 1.3 65.3 + - + +
134A SER 3.8 0.2 - - - -
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Residues in contact with GLN 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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71A PRO* 3.6 21.8 - - + +
90A LYS* 4.9 0.9 - - - -
129A ASN* 2.5 60.7 + - - +
132A MSE 1.3 84.3 - - + +
134A SER* 1.3 63.2 + - - +
135A HIS* 3.5 14.4 + - - -
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Residues in contact with SER 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A PRO* 3.4 5.9 - - - +
72A GLN 2.9 27.5 + - - -
90A LYS* 3.7 16.6 + - - -
130A TYR* 2.7 31.0 + - - -
131A ILE 4.1 2.8 + - - +
132A MSE 3.8 0.4 - - - -
133A GLN* 1.3 78.8 - - - +
135A HIS* 1.3 62.9 + - - +
136A SER 3.4 18.7 + - - -
137A LEU* 3.9 16.3 - - - +
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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
------------------------------------------------------------
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