Contacts of the helix formed by residues 101 - 121 (chain A) in PDB entry 4YC3
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 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A TYR 3.4 2.9 + - - -
100A MET* 1.3 74.1 - - - +
102A SER* 1.3 61.8 + - - +
103A SER* 2.8 40.1 + - - -
104A LEU* 2.9 31.6 + - + +
105A VAL* 3.1 9.5 + - - +
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Residues in contact with SER 102 (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 MET 3.2 4.6 + - - -
101A ASP* 1.3 73.6 + - - +
103A SER* 1.3 59.3 + - - +
104A LEU 3.3 0.2 - - - -
105A VAL* 3.6 15.7 - - - +
106A LYS* 3.2 28.4 + - - +
255A ASN* 5.0 14.1 - - - -
286A TYR* 4.1 4.7 + - - -
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Residues in contact with SER 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ASP* 2.8 18.8 + - - -
102A SER* 1.3 78.3 + - - +
104A LEU* 1.3 60.3 + - - +
106A LYS* 3.3 15.6 - - - +
107A SER* 3.0 26.3 + - - -
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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
----------------------------------------------------------
90A TYR* 4.6 11.4 - - + +
100A MET* 3.2 22.0 - - + -
101A ASP* 2.9 21.6 + - + +
103A SER* 1.3 79.8 + - - +
105A VAL* 1.3 59.7 + - - +
107A SER* 3.1 10.6 + - - +
108A TYR* 2.8 87.1 + - + +
140A GLY* 5.1 9.0 - - - +
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Residues in contact with VAL 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A MET* 3.3 27.1 - - + +
101A ASP 3.1 12.8 + - - +
102A SER* 3.6 15.5 - - - +
103A SER 3.4 0.2 - - - -
104A LEU* 1.3 73.8 - - - +
106A LYS* 1.3 56.8 + - - +
108A TYR* 3.9 1.3 - - - +
109A LEU* 2.9 30.3 + - - +
194A PHE* 4.0 17.9 - - + -
197A LEU* 3.9 35.6 - - + +
198A ALA* 4.4 13.9 - - + +
255A ASN 6.2 0.2 - - - +
256A LEU* 5.0 1.8 - - + -
286A TYR* 3.6 13.9 - - - +
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Residues in contact with LYS 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A SER* 3.2 14.1 + - - +
103A SER* 3.3 18.7 - - - +
105A VAL* 1.3 78.8 - - - +
107A SER* 1.3 56.2 + - - +
109A LEU 3.4 1.0 + - - -
110A TYR* 2.9 30.2 + - - +
257A ASP* 4.9 8.1 + - - -
286A TYR* 3.2 65.4 + - + +
287A PHE* 3.5 20.7 - - + +
288A ASN 5.3 2.6 + - - +
289A ASP* 5.4 12.8 + - + -
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Residues in contact with SER 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A SER 3.0 16.7 + - - -
104A LEU* 3.1 13.2 + - - +
106A LYS* 1.3 73.8 - - - +
108A TYR* 1.3 64.9 - - - +
110A TYR* 3.4 7.3 + - - +
111A GLN* 3.1 44.6 + - - +
140A GLY 4.5 3.8 + - - -
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Residues in contact with TYR 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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87A LEU* 4.2 12.6 - - + -
90A TYR* 4.6 10.1 - + - -
100A MET* 3.3 21.5 - - + -
104A LEU* 2.8 46.8 + - + +
105A VAL 4.0 2.9 - - - +
107A SER* 1.3 72.6 - - - +
109A LEU* 1.3 62.5 + - - +
111A GLN* 3.3 7.1 + - - -
112A ILE* 3.0 29.8 + - - +
136A ILE* 3.7 35.7 - - + +
137A ASP 4.8 2.4 + - - -
140A GLY* 3.6 28.7 - - - -
142A ILE* 3.7 32.9 - - + +
197A LEU* 4.0 16.2 - - + -
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Residues in contact with LEU 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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105A VAL 2.9 22.3 + - - +
106A LYS* 3.8 4.0 - - - +
108A TYR* 1.3 72.9 - - - +
110A TYR* 1.3 63.6 + - - +
112A ILE* 3.3 10.5 + - + +
113A LEU* 3.0 31.1 + - + +
190A ILE* 3.6 31.4 - - + +
193A ILE* 6.1 0.2 - - + -
194A PHE* 3.5 61.2 - - + +
197A LEU* 4.6 6.8 - - + +
263A LEU* 3.7 17.3 - - + -
267A MET* 4.6 3.6 - - + -
286A TYR* 4.0 1.8 - - + -
287A PHE* 4.0 11.2 - - + -
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Residues in contact with TYR 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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106A LYS 2.9 17.8 + - - +
107A SER* 3.6 8.7 - - - +
109A LEU* 1.3 75.1 - - - +
111A GLN* 1.3 60.1 + - + +
113A LEU* 3.3 4.9 + - - +
114A GLN* 3.0 69.5 + - - +
282A LEU* 3.7 42.7 + - + +
287A PHE* 3.5 35.1 - + + -
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Residues in contact with GLN 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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62A ASN* 3.3 32.1 + - - +
107A SER* 3.1 38.4 + - - +
108A TYR* 4.0 6.1 - - - +
109A LEU 3.3 0.2 - - - -
110A TYR* 1.3 75.4 - - + +
112A ILE* 1.3 66.1 + - - +
114A GLN* 3.2 15.2 + - - +
115A GLY 3.0 18.9 + - - -
140A GLY 3.2 16.5 + - - -
141A THR* 3.5 8.5 + - - +
142A ILE* 3.1 37.2 + - + -
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Residues in contact with ILE 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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87A LEU* 5.4 0.2 - - + -
108A TYR 3.0 27.8 + - - +
109A LEU* 3.6 11.9 - - + +
111A GLN* 1.3 75.1 - - - +
113A LEU* 1.3 65.5 + - - +
115A GLY* 3.1 3.5 + - - -
116A ILE* 2.9 21.2 + - + +
129A LEU* 5.4 2.7 - - + -
134A LEU* 3.8 34.3 - - + -
142A ILE* 4.0 21.3 - - + -
144A LEU* 3.9 17.5 - - + +
190A ILE* 3.7 34.5 - - + -
193A ILE* 4.7 6.7 - - + -
197A LEU* 4.6 13.7 - - + -
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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 LEU* 3.0 29.3 + - + +
110A TYR 3.6 0.2 - - - +
112A ILE* 1.3 77.9 - - - +
114A GLN* 1.3 56.2 + - - +
116A ILE* 3.3 4.2 + - + +
117A VAL* 2.8 35.7 + - - +
187A ILE* 4.8 2.7 - - + -
190A ILE* 4.1 21.8 - - + -
267A MET* 4.0 22.2 - - + -
278A GLY* 4.4 13.5 - - - +
281A ALA* 4.0 22.9 - - + -
282A LEU* 3.5 22.7 - - + -
287A PHE* 3.7 31.2 - - + -
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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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60A HIS* 3.8 14.3 + - + +
62A ASN* 3.7 15.2 - - - +
110A TYR* 3.0 49.1 + - + +
111A GLN* 3.5 13.9 - - - +
113A LEU* 1.3 77.4 - - - +
115A GLY* 1.3 61.8 + - - +
117A VAL* 3.8 5.7 - - - +
118A PHE* 3.1 23.7 + - - +
282A LEU* 4.0 20.2 - - + -
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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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60A HIS* 4.0 16.0 - - - -
62A ASN* 4.2 9.6 - - - -
63A ILE* 3.9 4.6 - - - +
111A GLN 3.0 14.3 + - - -
112A ILE 3.5 3.6 - - - -
114A GLN* 1.3 76.3 - - - +
116A ILE* 1.3 60.3 + - - +
118A PHE* 3.4 4.7 + - - +
119A CYS* 3.3 24.8 + - - -
144A LEU* 3.9 15.7 - - - -
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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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112A ILE 2.9 11.7 + - - +
113A LEU* 3.5 14.8 - - + +
115A GLY* 1.3 72.4 - - - +
117A VAL* 1.3 70.3 + - + +
119A CYS* 3.1 11.7 + - + +
120A HIS* 2.9 53.5 + - + +
126A HIS* 4.3 8.5 - - + -
129A LEU* 3.9 19.3 - - + -
144A LEU* 4.0 17.4 - - + +
186A ASP* 3.7 18.8 - - + +
187A ILE* 4.2 14.4 - - + -
190A ILE* 3.7 26.9 - - + -
278A GLY* 4.7 0.4 - - - -
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Residues in contact with VAL 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 22.3 + - - +
114A GLN* 3.8 4.9 - - - +
115A GLY 3.3 0.2 - - - -
116A ILE* 1.3 77.7 - - - +
118A PHE* 1.3 58.4 + - - +
120A HIS* 3.9 5.3 - - - +
121A SER* 2.6 43.0 + - - +
278A GLY* 3.5 37.0 - - - +
279A LYS* 3.6 15.9 - - + +
282A LEU* 4.0 16.2 - - + -
169B TYR* 4.1 10.5 - - + +
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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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57A GLU 3.6 16.2 - - - -
58A LEU* 4.0 6.5 - - + -
59A ARG* 3.0 34.8 - - + -
60A HIS* 3.3 27.8 - + + +
63A ILE* 4.1 15.3 - - + -
114A GLN 3.1 12.3 + - - +
115A GLY 3.5 9.9 - - - +
117A VAL* 1.3 80.1 - - - +
119A CYS* 1.3 63.4 - - - +
121A SER* 3.5 3.9 + - - -
122A ARG* 2.9 75.3 + - - +
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Residues in contact with CYS 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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58A LEU* 4.4 9.0 - - - -
63A ILE* 3.8 20.2 - - - -
115A GLY 3.3 13.7 + - - -
116A ILE* 3.1 14.6 + - + +
118A PHE* 1.3 78.9 - - - +
120A HIS* 1.3 63.5 + - + +
122A ARG* 3.0 13.2 + - - -
124A VAL* 3.0 45.4 + - + +
125A LEU* 5.7 0.2 - - - -
126A HIS* 5.8 0.9 - - - +
144A LEU* 4.3 7.9 - - - -
147A PHE* 4.0 25.1 - - - -
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Residues in contact with HIS 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* 2.9 42.6 + - + +
117A VAL 3.4 0.4 + - - +
119A CYS* 1.3 76.9 - - + +
121A SER* 1.3 59.9 - - - +
122A ARG 3.1 1.3 + - - -
123A ARG* 3.3 11.7 + - - +
124A VAL 3.3 20.0 - - - +
125A LEU* 4.1 4.3 - - + +
183A THR* 3.6 50.8 - - + +
186A ASP* 3.0 26.1 + - + +
187A ILE* 4.3 9.8 - - + +
278A GLY 5.3 0.2 + - - -
169B TYR* 3.9 41.1 + - + +
173B ILE* 4.2 4.2 - - - +
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Residues in contact with SER 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 VAL* 2.6 29.3 + - - +
118A PHE* 3.7 6.0 - - - -
119A CYS 3.1 0.4 - - - -
120A HIS* 1.3 75.3 - - - +
122A ARG* 1.3 72.5 + - - +
123A ARG 3.5 0.7 - - - -
279A LYS* 5.7 0.2 - - - +
169B TYR* 3.6 19.8 - - - -
172B ASP* 3.7 25.2 + - - +
173B ILE* 3.5 26.2 + - - -
176B TYR* 4.2 2.1 - - - +
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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