Contacts of the helix formed by residues 115 - 132 (chain A) in PDB entry 4KYI
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 GLY 115 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ASP* 3.4 6.9 + - - -
113A ALA 3.4 3.0 - - - -
114A ARG* 1.3 77.7 - - - +
116A ASP* 1.3 62.3 + - - +
117A ARG 3.5 1.6 - - - -
118A PHE 4.4 3.4 - - - -
119A ARG* 3.4 10.6 + - - +
266A GLN* 3.2 42.6 - - - +
275A PHE* 3.7 19.2 - - - -
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Residues in contact with ASP 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ASP* 4.1 7.0 - - - +
114A ARG* 3.2 29.4 - - + +
115A GLY* 1.3 81.7 - - - +
117A ARG* 1.3 56.5 + - - +
119A ARG* 2.4 35.0 + - - +
120A ASN* 2.7 38.1 + - - -
190A ASP* 5.1 1.1 - - - +
194A ASN* 3.7 23.6 + - - +
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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
----------------------------------------------------------
102A LYS 4.7 2.8 + - - -
103A LEU* 4.0 29.2 - - + +
104A LEU 4.4 7.5 + - - -
105A ASP* 3.2 36.9 + - - +
115A GLY 3.5 0.2 - - - -
116A ASP* 1.3 74.5 - - - +
118A PHE* 1.3 65.0 + - - +
119A ARG 3.1 1.3 - - - -
120A ASN* 3.1 12.2 + - - +
121A ILE* 3.2 16.9 + - + +
183A VAL* 4.3 11.5 - - - +
186A LEU* 3.5 42.2 - - + +
187A GLU* 3.5 36.4 + - - +
189A LEU* 5.4 1.5 - - + +
190A ASP* 3.3 32.2 + - - +
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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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77A MET* 4.0 27.4 - - + -
98A LEU* 6.0 0.7 - - + -
100A ILE* 3.5 37.5 - - + -
103A LEU* 3.8 38.5 + - + +
115A GLY* 4.3 2.5 + - - +
117A ARG* 1.3 78.5 - - - +
119A ARG* 1.3 61.6 + - - +
120A ASN 3.4 0.3 + - - -
121A ILE* 3.6 2.6 + - + +
122A LEU* 3.2 47.7 + - + +
265A VAL* 4.6 5.2 - - + -
266A GLN* 3.7 34.5 - - + -
269A GLY* 5.6 7.4 - - - -
275A PHE* 4.4 20.4 - + + -
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Residues in contact with ARG 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A GLY 3.4 18.9 + - - +
116A ASP* 2.4 40.9 + - - +
117A ARG 3.1 0.4 - - - -
118A PHE* 1.3 81.0 - - - +
120A ASN* 1.3 88.7 + - - +
122A LEU* 3.6 2.3 - - - +
123A ASP* 3.3 17.3 + - - +
194A ASN* 3.0 20.0 + - - +
198A THR* 5.9 4.8 - - - +
212A ARG* 4.1 26.8 - - - +
262A ALA* 3.3 48.6 - - - +
263A GLN* 4.1 14.3 - - - +
266A GLN* 4.1 9.8 + - + +
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Residues in contact with ASN 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 ASP 2.7 24.0 + - - +
117A ARG* 3.1 7.6 + - - +
119A ARG* 1.3 101.3 + - - +
121A ILE* 1.3 64.0 + - - +
122A LEU 3.2 1.6 - - - -
123A ASP* 3.4 6.1 + - - +
124A VAL* 3.1 27.7 + - - +
189A LEU* 4.1 14.4 - - + -
190A ASP* 3.4 28.3 + - - +
193A LEU* 3.6 34.2 - - + +
194A ASN* 3.8 9.7 + - - +
212A ARG* 4.9 0.9 + - - -
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Residues in contact with ILE 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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98A LEU* 4.8 7.2 - - + -
103A LEU* 3.7 35.4 - - + -
117A ARG* 3.2 13.8 + - + +
118A PHE 3.6 3.8 + - - +
120A ASN* 1.3 73.0 - - - +
122A LEU* 1.3 62.6 + - + +
124A VAL* 3.3 5.2 + - + +
125A ILE* 2.9 38.1 + - + +
176A ILE* 4.0 20.0 - - + -
179A LEU* 4.7 10.1 - - + -
180A THR* 4.1 19.7 - - + -
186A LEU* 4.3 11.2 - - + -
189A LEU* 3.7 24.0 - - + -
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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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77A MET* 4.2 30.3 - - + -
81A ILE* 6.1 0.4 - - + -
118A PHE* 3.2 35.0 + - + +
119A ARG* 3.6 7.0 - - - +
120A ASN 3.2 0.4 - - - -
121A ILE* 1.3 80.2 - - + +
123A ASP* 1.3 56.6 + - - +
125A ILE* 3.3 11.2 + - + +
126A TYR* 2.9 55.6 + - + +
262A ALA* 3.6 27.1 - - + +
265A VAL* 3.6 24.5 - - + -
266A GLN* 3.8 7.4 - - + +
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Residues in contact with ASP 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 ARG* 3.3 11.2 + - - +
120A ASN* 3.7 10.8 - - - +
121A ILE 3.3 0.4 - - - -
122A LEU* 1.3 78.6 - - - +
124A VAL* 1.3 57.9 + - - +
126A TYR* 3.8 8.3 - - - +
127A MET* 2.8 33.5 + - - +
159A TYR* 2.9 36.5 + - + -
193A LEU* 4.4 6.8 - - + +
212A ARG* 3.4 27.2 + - - -
213A LEU* 4.8 7.3 + - - +
260A SER* 4.5 3.1 + - - -
262A ALA* 3.4 22.8 + - - +
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Residues in contact with VAL 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 ASN 3.1 15.9 + - - +
121A ILE* 3.6 9.4 - - - +
122A LEU 3.3 0.2 - - - -
123A ASP* 1.3 74.1 - - - +
125A ILE* 1.3 64.6 + - - +
127A MET* 3.3 10.3 - - + +
128A MET* 3.0 23.7 + - - +
159A TYR* 6.1 0.4 - - + -
163A LEU* 4.6 13.7 - - + -
170A ILE* 3.7 33.9 - - + -
176A ILE* 3.8 17.9 - - + -
179A LEU* 4.8 6.5 - - + -
189A LEU* 4.2 26.5 - - + -
193A LEU* 4.4 6.1 - - + -
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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
----------------------------------------------------------
77A MET* 4.8 7.4 - - + -
81A ILE* 4.1 12.1 - - + -
84A VAL* 5.6 1.1 - - + -
86A MET* 3.7 26.7 - - + +
94A LEU* 3.8 31.2 - - + -
98A LEU* 4.5 5.4 - - + -
121A ILE* 2.9 33.5 + - + +
122A LEU* 3.3 14.3 + - + +
124A VAL* 1.3 75.5 - - - +
126A TYR* 1.3 74.9 + - + +
128A MET* 3.5 2.9 + - - +
129A GLN* 3.3 22.0 + - - +
176A ILE* 3.7 27.4 - - + -
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Residues in contact with TYR 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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80A SER* 2.7 46.7 + - - -
81A ILE* 4.4 3.6 - - + -
84A VAL* 4.5 12.6 - - + -
122A LEU* 2.9 35.2 + - + +
123A ASP* 3.8 10.1 - - - +
125A ILE* 1.3 90.2 - - + +
127A MET* 1.3 52.8 + - - +
129A GLN* 3.2 1.7 + - - +
130A MET* 2.7 48.9 + - - +
213A LEU* 4.3 11.9 - - + -
261A ILE* 3.5 39.5 - - + -
262A ALA* 3.6 17.7 - - + -
265A VAL* 3.5 18.2 - - - +
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Residues in contact with MET 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ASP 2.8 28.6 + - - +
124A VAL* 3.3 15.9 - - - +
126A TYR* 1.3 74.0 - - - +
128A MET* 1.3 65.6 + - - +
130A MET* 4.5 0.9 - - - +
131A LYS* 3.1 29.5 + - + +
156A ILE* 3.8 19.5 - - + +
159A TYR* 3.6 37.7 - - + -
160A GLU* 3.6 29.4 - - + +
163A LEU* 4.5 15.5 - - + -
170A ILE* 4.7 12.8 - - - +
213A LEU* 3.8 21.0 - - + +
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Residues in contact with MET 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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86A MET* 5.0 4.7 - - + -
124A VAL 3.0 18.2 + - - +
125A ILE 3.8 4.5 - - - +
127A MET* 1.3 83.9 - - - +
129A GLN* 1.3 89.5 + - + +
131A LYS* 3.8 3.1 + - - +
132A LYS* 3.3 38.0 + - + +
170A ILE* 3.9 29.4 - - + +
171A ASN* 4.2 9.0 - - - +
172A ASN* 3.3 35.9 - - - +
173A VAL* 3.7 20.2 - - + -
176A ILE* 4.2 7.9 - - + -
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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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84A VAL* 3.8 39.3 - - + +
85A GLY 4.0 5.1 + - - -
86A MET* 3.9 26.6 - - + +
87A ASP* 4.8 2.8 - - - +
90A ASP* 4.2 8.0 + - - +
125A ILE 3.3 12.4 + - - +
126A TYR 3.2 1.6 + - - -
128A MET* 1.3 96.3 - - + +
130A MET* 1.3 60.2 - - - +
131A LYS 3.1 5.9 + - - -
132A LYS* 3.6 16.2 + - - +
133A HIS* 3.3 50.7 + - - -
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Residues in contact with MET 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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84A VAL* 3.6 17.3 - - + -
126A TYR* 2.7 28.9 + - - +
127A MET* 4.1 1.6 - - - +
129A GLN* 1.3 71.6 - - - +
131A LYS* 1.3 60.6 + - - +
133A HIS* 4.0 1.3 + - - -
134A LEU* 3.8 21.8 + - - +
152A LEU* 4.9 4.7 - - + +
156A ILE* 4.2 7.3 - - + +
213A LEU* 3.7 37.0 - - + -
217A ASP* 3.7 41.1 - - + +
218A LEU* 4.1 17.7 - - + -
221A LEU* 3.8 31.9 - - + +
261A ILE* 4.6 3.1 - - - -
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Residues in contact with LYS 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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127A MET* 3.1 21.4 + - + +
128A MET* 3.9 5.8 - - - +
129A GLN 3.1 0.6 - - - -
130A MET* 1.3 77.6 - - - +
132A LYS* 1.3 59.5 + - + +
133A HIS 3.0 4.5 - - - -
134A LEU* 3.0 22.1 + - + +
135A GLU* 3.3 47.3 + - - +
153A LYS* 4.7 19.8 - - - +
156A ILE* 3.7 30.5 - - + +
160A GLU* 3.3 26.8 + - - +
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Residues in contact with LYS 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 ASP* 4.4 14.6 + - - -
128A MET* 3.3 36.2 + - + +
129A GLN* 3.6 21.2 + - - +
131A LYS* 1.3 77.9 - - + +
133A HIS* 1.3 64.1 + - + +
135A GLU* 4.1 23.8 - - - +
136A SER* 4.2 12.8 + - - -
171A ASN* 4.6 16.8 + - + +
172A ASN* 6.0 1.2 - - - +
173A VAL* 5.3 3.0 - - - +
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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
------------------------------------------------------------
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