Contacts of the helix formed by residues 103 - 120 (chain A) in PDB entry 2CUY
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 GLU 103 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ARG* 5.6 2.2 - - - +
102A LEU* 1.3 80.1 - - - +
104A LEU* 1.3 65.8 + - - +
105A GLU* 4.6 11.7 - - - +
106A ASP* 3.3 25.3 + - - +
107A ALA* 3.0 21.2 + - - +
213A PRO* 5.3 8.6 + - + +
215A ARG* 6.4 1.8 - - - -
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Residues in contact with LEU 104 (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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30A VAL* 3.7 37.2 - - + +
33A ARG* 3.9 36.3 - - + +
64A LEU* 3.7 25.8 - - + -
65A ALA* 4.9 2.9 - - - -
68A TYR* 4.0 21.3 - - + -
97A VAL* 3.9 15.9 - - + +
102A LEU 3.7 1.8 + - - -
103A GLU* 1.3 72.1 - - - +
105A GLU* 1.3 71.9 + - - +
107A ALA* 3.0 5.0 + - - +
108A LEU* 2.9 42.1 + - + +
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Residues in contact with GLU 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ARG* 3.0 57.2 + - - +
37A ALA* 4.0 25.0 - - + +
103A GLU* 3.4 11.6 - - - +
104A LEU* 1.3 78.1 + - + +
106A ASP* 1.3 62.3 + - - +
108A LEU* 3.5 3.4 + - - +
109A ARG* 3.1 51.2 + - - +
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Residues in contact with ASP 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A LEU* 3.6 19.3 - - + -
103A GLU* 3.3 26.1 + - + +
104A LEU 3.3 0.6 - - - -
105A GLU* 1.3 77.1 - - - +
107A ALA* 1.3 57.5 + - - +
109A ARG* 2.8 27.5 + - - +
110A LEU* 2.9 33.8 + - - +
212A VAL* 4.0 26.0 - - + +
213A PRO* 4.3 12.7 - - - +
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Residues in contact with ALA 107 (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 LEU* 4.0 11.7 - - + -
93A TRP* 5.0 1.6 - - + -
97A VAL* 3.3 32.3 - - + -
102A LEU* 3.7 19.9 - - + +
103A GLU 3.0 8.8 + - - +
104A LEU 3.0 8.5 + - - +
106A ASP* 1.3 77.7 - - - +
108A LEU* 1.3 62.3 + - - +
110A LEU* 3.1 5.0 + - - +
111A VAL* 2.9 29.5 + - - +
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Residues in contact with LEU 108 (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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33A ARG 4.9 0.2 - - - +
34A ALA* 3.6 34.8 - - + +
37A ALA* 4.3 11.7 - - + -
38A LEU* 4.0 15.4 - - + +
41A LEU* 4.4 4.9 - - + -
61A PRO* 3.2 37.2 - - + +
64A LEU* 3.9 14.1 - - + -
65A ALA* 4.0 8.3 - - + -
104A LEU* 2.9 37.6 + - + +
105A GLU* 3.8 3.8 - - - +
107A ALA* 1.3 75.9 - - - +
109A ARG* 1.3 64.1 + - - +
111A VAL* 3.4 6.2 - - - +
112A ARG* 3.1 24.3 + - - +
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Residues in contact with ARG 109 (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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37A ALA* 4.4 17.2 + - + +
38A LEU* 4.5 20.2 - - + +
105A GLU* 3.1 45.0 + - - +
106A ASP* 2.8 31.6 + - - +
108A LEU* 1.3 76.4 - - - +
110A LEU* 1.3 63.3 + - + +
112A ARG* 3.4 3.8 + - - +
113A LEU* 3.2 31.9 + - + +
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Residues in contact with LEU 110 (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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93A TRP* 3.5 32.8 - - + -
102A LEU* 4.3 12.6 - - + -
106A ASP 2.9 20.8 + - - +
107A ALA 3.5 3.8 - - - +
109A ARG* 1.3 79.5 - - + +
111A VAL* 1.3 56.0 + - - +
113A LEU* 3.2 8.9 + - + +
114A ARG* 2.8 27.0 + - - +
205A LEU* 3.7 13.5 - - + +
208A ASP* 4.0 18.4 - - + +
209A LEU* 3.8 40.6 - - + +
212A VAL* 3.8 18.2 - - + -
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Residues in contact with VAL 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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60A GLN* 3.3 14.0 - - + +
61A PRO* 3.7 25.8 - - + -
64A LEU* 4.2 7.4 - - + -
90A LEU* 3.4 30.3 - - + -
93A TRP* 3.8 34.5 - - + -
107A ALA 2.9 26.2 + - - +
108A LEU* 3.4 13.7 - - - +
110A LEU* 1.3 71.3 - - - +
112A ARG* 1.3 61.5 + - - +
114A ARG* 3.8 6.1 - - - -
115A GLY* 2.8 26.0 + - - -
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Residues in contact with ARG 112 (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 LEU* 3.8 43.9 - - + +
39A PRO 5.0 4.8 + - - -
41A LEU* 4.5 11.1 - - - +
44A LEU* 4.6 5.1 - - - +
57A GLU* 3.2 36.3 + - + +
58A ASN* 3.0 29.7 + - - +
61A PRO* 4.2 11.2 - - + +
108A LEU 3.1 18.1 + - - +
109A ARG* 3.7 5.8 - - - +
111A VAL* 1.3 78.7 - - - +
113A LEU* 1.3 68.6 + - + +
115A GLY* 3.4 1.0 + - - -
116A ARG* 3.0 24.5 + - + +
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Residues in contact with LEU 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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109A ARG* 3.2 21.2 + - + +
110A LEU* 3.4 11.7 - - + +
111A VAL 3.1 0.2 - - - -
112A ARG* 1.3 81.7 - - + +
114A ARG* 1.3 59.6 + - - +
116A ARG* 3.1 20.6 + - - +
117A TYR* 2.8 59.5 + - + +
205A LEU* 4.3 2.7 - - + -
208A ASP* 3.6 35.7 - - + +
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Residues in contact with ARG 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLN* 4.9 1.4 + - - +
60A GLN* 2.8 44.7 + - - +
89A SER* 2.8 26.3 + - - -
90A LEU* 3.7 18.7 - - - +
93A TRP* 3.5 29.1 - - - +
110A LEU 2.8 21.1 + - - +
111A VAL* 3.5 9.4 - - - +
113A LEU* 1.3 72.4 - - - +
115A GLY* 1.3 57.8 + - - +
117A TYR* 3.6 5.1 - - - +
118A MET* 2.8 59.5 + - + +
194A HIS* 4.1 1.8 + - - -
205A LEU* 4.0 18.1 - - + +
243A GLN* 2.9 19.6 + - - -
244A ILE* 3.1 22.2 - - + +
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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
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56A THR* 3.6 19.9 - - - +
57A GLU* 4.3 3.8 - - - -
60A GLN* 3.5 23.3 + - - -
111A VAL 2.8 18.9 + - - -
112A ARG 3.8 1.1 - - - -
114A ARG* 1.3 73.5 - - - +
116A ARG* 1.3 62.0 + - - +
118A MET* 3.6 2.2 - - - +
119A GLN* 2.9 25.1 + - - +
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Residues in contact with ARG 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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57A GLU* 3.5 29.4 - - + +
112A ARG* 3.0 16.3 + - + +
113A LEU* 3.6 19.8 - - - +
115A GLY* 1.3 75.5 - - - +
117A TYR* 1.3 88.9 + - - +
119A GLN* 3.3 6.1 + - - +
120A GLU* 2.9 68.7 + - - +
204A ARG* 4.1 7.5 - - - +
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Residues in contact with TYR 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 LEU* 2.8 42.6 + - + +
114A ARG* 3.6 4.9 - - - +
116A ARG* 1.3 100.3 + - - +
118A MET* 1.3 63.3 - - - +
120A GLU* 3.5 3.1 + - - +
121A ALA* 3.2 23.2 + - - +
201A ALA* 3.7 21.7 - - + +
204A ARG* 3.3 55.9 + - + +
205A LEU* 3.7 23.3 - - + -
208A ASP* 2.8 32.7 + - - -
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Residues in contact with MET 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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9A GLN* 4.8 0.4 - - - +
60A GLN* 3.6 13.2 - - - -
89A SER* 5.2 0.4 - - - +
114A ARG* 2.8 55.7 + - + +
115A GLY* 3.6 4.3 - - - +
117A TYR* 1.3 79.0 - - - +
119A GLN* 1.3 62.1 + - - +
121A ALA* 3.4 15.4 + - - +
122A VAL* 4.6 0.9 + - - +
191A ALA* 3.9 10.0 - - - +
193A PHE* 3.8 22.7 - - + -
194A HIS* 5.1 5.2 - - - +
198A MET* 3.1 31.4 - - + +
201A ALA* 3.8 9.4 - - + -
244A ILE* 3.4 45.8 - - + +
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Residues in contact with GLN 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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55A LEU* 6.6 0.7 - - + -
56A THR* 3.0 29.2 + - - +
57A GLU 5.9 0.4 - - - +
115A GLY 2.9 17.2 + - - +
116A ARG* 3.3 6.0 + - - +
118A MET* 1.3 78.9 - - - +
120A GLU* 1.3 58.1 + - - +
121A ALA 3.2 4.0 + - - -
122A VAL 3.7 13.9 + - - +
124A VAL* 5.1 9.5 - - - +
190A SER* 2.6 31.3 + - - -
191A ALA* 4.2 16.5 - - - +
193A PHE* 4.8 1.6 - - - -
178B LYS* 6.0 0.3 + - - -
183B ARG* 5.7 7.0 - - - +
184B VAL 5.8 3.7 + - - +
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Residues in contact with GLU 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 ARG* 2.9 51.5 + - - +
117A TYR 3.7 1.6 - - - +
119A GLN* 1.3 75.3 - - + +
121A ALA* 1.3 61.3 + - - +
122A VAL 3.5 3.6 - - - +
204A ARG* 2.5 35.2 + - - +
178B LYS* 6.3 1.3 - - - +
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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
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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