Contacts of the helix formed by residues 111 - 126 (chain A) in PDB entry 5M64
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 LYS 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A LEU* 1.3 81.6 - - + +
112A SER* 1.3 59.6 + - - +
113A VAL* 3.1 26.8 + - + +
114A GLU* 3.2 28.7 + - + +
115A VAL* 2.9 29.7 + - - +
230A ARG* 4.3 8.9 - - - +
234A ASP* 3.0 34.9 + - + -
235A ASN* 3.6 11.0 - - - +
7T A 5.4 7.3 + - - -
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Residues in contact with SER 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LYS* 1.3 73.8 - - - +
113A VAL* 1.3 57.6 + - - +
115A VAL* 3.9 8.7 - - - -
116A HIS* 3.0 30.8 + - - +
182A LYS* 3.3 13.0 - - - -
235A ASN* 4.2 9.5 + - - +
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Residues in contact with VAL 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LYS* 3.0 17.2 - - + -
112A SER* 1.3 79.7 - - - +
114A GLU* 1.3 60.4 + - - +
116A HIS* 3.8 1.6 - - - +
117A ARG* 2.9 26.6 + - + +
178A LEU* 3.6 36.6 - - + -
181A LEU* 4.8 8.3 - - + -
182A LYS* 3.5 18.1 - - - +
185A ARG* 4.1 17.6 + - - +
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Residues in contact with GLU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LEU* 5.1 9.2 - - + -
111A LYS* 3.2 27.0 + - + +
113A VAL* 1.3 79.5 - - - +
115A VAL* 1.3 61.3 + - - +
117A ARG* 3.3 14.3 - - - +
118A TYR* 3.0 74.6 + - + +
226A LYS* 4.6 8.7 - - - +
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Residues in contact with VAL 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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108A PHE* 4.3 25.8 - - + +
110A LEU* 3.7 24.5 - - + +
111A LYS 2.9 22.8 + - - +
112A SER* 4.3 6.1 - - - -
114A GLU* 1.3 77.1 - - - +
116A HIS* 1.3 59.1 + - - +
118A TYR* 4.0 5.7 - - - +
119A ALA* 2.9 28.9 + - - +
331A GLU* 5.4 4.9 - - + +
334A VAL* 4.4 28.3 - - + +
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Residues in contact with HIS 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A SER* 3.0 23.1 + - - +
115A VAL* 1.3 75.2 - - - +
117A ARG* 1.3 59.8 + - - +
119A ALA* 3.7 7.4 - - + -
120A CYS* 2.8 36.9 + - + +
182A LYS* 3.6 35.6 - - + +
185A ARG* 3.6 35.4 + - + +
186A SER* 5.1 2.4 - - - -
333A CYS* 4.7 19.2 - - - -
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Residues in contact with ARG 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A VAL* 2.9 19.7 + - + +
114A GLU* 3.2 29.4 + - - +
116A HIS* 1.3 77.7 - - - +
118A TYR* 1.3 63.9 + - + +
120A CYS* 3.3 5.1 + - - +
121A LYS* 2.9 33.2 + - + +
136A LEU* 2.3 63.1 + - - +
137A ASP* 3.5 25.9 + - - +
139A ILE 5.1 1.0 + - - -
184A LYS* 4.9 1.0 - - - +
185A ARG* 3.1 60.9 - - - +
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Residues in contact with TYR 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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110A LEU* 6.0 1.6 - - + -
114A GLU* 3.0 48.0 + - + +
115A VAL* 4.1 4.5 - - - +
117A ARG* 1.3 82.5 - - + +
119A ALA* 1.3 57.7 + - - +
121A LYS* 4.6 9.2 - - + +
122A LEU* 3.0 36.9 + - - +
219A LEU* 4.5 8.5 - - + -
222A GLU* 3.3 22.4 + - - -
223A PHE* 3.4 38.8 - + + -
226A LYS* 2.5 47.3 + - + -
334A VAL* 5.5 2.7 - - + -
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Residues in contact with ALA 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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115A VAL* 2.9 19.9 + - + +
116A HIS* 3.9 10.5 - - + +
118A TYR* 1.3 76.7 - - - +
120A CYS* 1.3 58.2 + - - +
122A LEU* 4.0 4.9 - - - +
123A ARG* 3.1 32.0 + - - +
333A CYS* 4.7 11.2 - - - +
334A VAL* 3.7 36.9 - - + +
337A TYR* 5.6 2.6 - - - +
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Residues in contact with CYS 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 HIS* 2.8 34.3 + - + +
117A ARG* 3.8 11.7 - - - +
119A ALA* 1.3 75.3 - - - +
121A LYS* 1.3 65.2 + - - +
122A LEU 3.2 1.1 - - - -
123A ARG* 3.0 17.4 + - - +
124A LEU* 3.1 14.4 + - - +
136A LEU* 3.8 2.8 - - - +
185A ARG* 3.6 29.4 - - + -
186A SER* 4.9 0.9 - - - -
189A VAL* 3.5 31.0 - - - +
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Residues in contact with LYS 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 ARG* 2.9 25.2 + - + +
118A TYR* 4.1 9.0 - - + +
120A CYS* 1.3 76.5 - - - +
122A LEU* 1.3 64.0 + - + +
124A LEU* 3.3 6.9 + - - +
125A LEU* 3.1 25.8 + - + +
130A ILE* 5.9 0.2 - - - +
133A SER* 3.1 48.1 + - - +
134A TYR* 3.3 27.6 - - - -
136A LEU* 3.8 15.1 - - + +
137A ASP* 5.8 8.4 - - + +
215A GLU* 6.2 0.2 - - - -
219A LEU* 4.3 35.0 - - + -
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Residues in contact with LEU 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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118A TYR* 3.0 26.8 + - - +
119A ALA* 4.3 4.7 - - - +
121A LYS* 1.3 79.2 - - + +
123A ARG* 1.3 57.6 + - - +
124A LEU 3.0 5.4 - - - -
125A LEU* 3.1 18.9 + - + -
126A GLN* 2.8 17.0 - - - +
216A ARG* 5.6 7.6 - - + +
219A LEU* 3.8 34.1 - - + -
220A VAL* 6.0 0.7 - - + +
223A PHE* 3.7 29.8 - - + -
334A VAL* 6.3 2.2 - - + -
337A TYR* 3.0 43.2 - - + -
338A VAL* 5.2 11.4 - - + -
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Residues in contact with ARG 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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119A ALA 3.1 23.8 + - - +
120A CYS* 3.0 15.4 + - - +
122A LEU* 1.3 76.0 - - - +
124A LEU* 1.3 51.1 + - - +
126A GLN* 2.5 34.7 + - - +
189A VAL* 4.6 14.7 - - + +
193A ILE* 4.6 1.4 - - - +
333A CYS* 2.4 51.2 + - - +
336A GLN* 5.2 3.4 - - - +
337A TYR* 4.4 21.2 - - - +
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Residues in contact with LEU 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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120A CYS 3.1 10.1 + - - +
121A LYS 3.7 5.8 - - - +
122A LEU 3.0 0.6 - - - -
123A ARG* 1.3 78.1 - - - +
125A LEU* 1.3 59.1 + - - +
126A GLN* 3.4 4.6 + - - +
127A TYR* 4.0 6.8 + - - +
129A LEU* 3.5 44.0 - - + +
132A GLU* 3.7 24.0 - - + +
133A SER* 3.7 8.3 - - - +
136A LEU* 3.7 22.4 - - + -
188A TYR* 5.2 1.3 - - + -
189A VAL* 4.0 12.6 - - + -
192A ALA* 4.0 19.3 - - + -
193A ILE* 3.7 28.6 - - + +
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Residues in contact with LEU 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 LYS* 3.1 18.2 + - - +
122A LEU* 3.1 24.0 + - + +
124A LEU* 1.3 75.4 - - - +
126A GLN* 1.3 64.2 + - - +
127A TYR 3.1 12.5 - - - +
129A LEU 5.0 0.9 - - - +
130A ILE* 4.1 23.3 - - + +
133A SER* 4.0 25.4 - - - -
212A VAL* 4.6 17.3 - - + +
215A GLU* 4.1 20.4 - - + +
216A ARG* 3.7 31.3 - - + +
219A LEU* 5.0 5.4 - - + -
337A TYR* 3.7 4.4 + - - +
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Residues in contact with GLN 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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122A LEU 2.8 19.6 - - - +
123A ARG* 2.5 31.0 + - - +
124A LEU* 4.2 1.9 - - - +
125A LEU* 1.3 72.6 - - - +
127A TYR* 1.3 93.5 + - + +
193A ILE* 4.8 3.0 - - - +
206A GLY* 4.7 2.0 - - - -
207A SER 2.9 23.0 + - - +
208A PHE* 5.7 1.4 - - - -
212A VAL* 5.6 2.1 - - - +
216A ARG* 5.5 1.6 - - - +
337A TYR* 3.1 31.5 + - + +
341A SER 4.1 15.4 - - - +
343A PRO* 4.3 22.3 - - + +
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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