Contacts of the helix formed by residues 111 - 126 (chain B) in PDB entry 1P4A
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A PRO* 4.6 11.7 - - + +
107B ASP* 3.4 37.7 + - - +
108B ILE* 3.4 13.8 + - - +
109B LEU 3.5 0.2 - - - -
110B GLY* 1.3 77.1 - - - +
112B PRO* 1.3 68.1 - - + +
113B SER* 4.6 5.2 - - - +
114B VAL* 3.3 23.3 + - + +
115B LEU* 2.9 31.7 + - - +
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Residues in contact with PRO 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A TYR* 5.9 2.5 - - + -
149A ALA* 5.7 0.7 - - + -
150A SER* 4.4 24.0 - - - +
153A ASN* 3.7 26.0 - - - +
154A VAL* 3.6 35.7 - - - +
155A PRO* 4.0 3.6 - - + -
110B GLY 3.8 1.7 - - - +
111B LYS* 1.3 85.8 - - + +
113B SER* 1.3 68.4 + - - +
115B LEU* 3.3 7.9 + - + +
116B SER* 3.0 27.9 + - - -
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Residues in contact with SER 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ASN* 5.1 5.3 - - - +
111B LYS* 4.7 6.6 - - - +
112B PRO* 1.3 83.6 - - - +
114B VAL* 1.3 73.6 + - - +
116B SER* 3.1 18.1 + - - -
117B LYS* 3.4 16.5 + - - +
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Residues in contact with VAL 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B PHE* 3.8 13.1 - - + -
87B LEU* 4.5 13.2 - - + -
108B ILE* 3.7 37.0 - - + +
111B LYS* 3.3 29.1 + - + +
112B PRO 3.3 0.4 - - - -
113B SER* 1.3 86.5 + - - +
115B LEU* 1.3 66.2 + - + +
117B LYS* 3.3 5.2 + - - +
118B VAL* 3.1 32.1 + - + +
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Residues in contact with LEU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A TYR* 2.9 44.9 - - + -
108B ILE 4.7 1.6 - - - +
109B LEU* 3.4 19.3 - - + +
111B LYS 2.9 21.8 + - - +
112B PRO* 3.8 5.2 - - + +
114B VAL* 1.3 80.2 - - + +
116B SER* 1.3 56.8 + - - +
118B VAL* 3.3 4.1 + - - +
119B GLY 2.8 27.2 + - - -
143B PRO* 3.8 24.7 - - + +
144B LEU* 3.3 31.6 - - + -
146B TYR* 6.2 0.7 - - + -
147B ALA* 3.5 13.8 - - + +
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Residues in contact with SER 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B PRO 3.0 14.4 + - - -
113B SER* 3.1 14.4 + - - -
114B VAL 3.3 0.2 - - - -
115B LEU* 1.3 76.5 - - - +
117B LYS* 1.3 63.5 + - - +
120B LYS* 2.9 30.0 + - - +
147B ALA* 4.8 3.1 - - - +
151B TYR* 3.3 27.4 + - - -
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Residues in contact with LYS 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B MET* 3.5 13.7 - - + +
79B GLU* 2.9 27.1 + - - +
83B PHE* 3.5 41.7 - - + -
113B SER* 3.4 15.2 + - - +
114B VAL 3.3 1.9 + - - +
115B LEU 3.3 0.2 - - - -
116B SER* 1.3 80.8 + - - +
118B VAL* 1.3 57.9 + - - +
120B LYS* 3.3 12.1 + - + +
121B LEU* 2.8 30.3 + - - +
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Residues in contact with VAL 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B PHE* 3.7 20.9 - - + -
87B LEU* 4.5 2.0 - - + -
114B VAL* 3.1 23.7 + - + +
115B LEU 3.8 5.4 - - - +
117B LYS* 1.3 74.7 - - - +
119B GLY* 1.3 65.6 + - - +
121B LEU* 3.2 5.6 + - - +
122B PHE* 2.9 47.8 + - + -
144B LEU* 4.0 22.4 - - + -
232B LEU* 4.1 22.0 - - + -
249B LEU* 4.1 12.8 - - + -
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Residues in contact with GLY 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B LEU 2.8 20.9 + - - -
116B SER 3.9 0.9 - - - -
118B VAL* 1.3 73.6 - - - +
120B LYS* 1.3 57.2 + - - +
122B PHE* 3.3 4.9 + - - +
123B ALA* 2.9 29.1 + - - +
144B LEU 4.8 0.9 - - - -
147B ALA* 3.8 7.5 - - - +
148B ALA* 3.7 29.0 - - - -
151B TYR* 3.7 7.2 - - - -
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Residues in contact with LYS 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B GLY 2.9 25.4 + - - -
56B ILE* 3.3 20.2 + - - +
71B TYR* 5.4 0.8 + - - +
73B PRO* 4.6 8.5 - - + +
74B LYS 3.2 24.7 - - - +
75B MET* 4.0 22.0 - - + +
79B GLU* 4.4 6.1 + - - -
116B SER 2.9 19.8 + - - +
117B LYS* 3.6 13.4 - - + +
119B GLY* 1.3 72.3 - - - +
121B LEU* 1.3 62.0 + - - +
123B ALA* 3.2 1.7 + - - +
124B SER* 2.7 31.8 + - - -
151B TYR* 3.6 35.1 - - + +
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Residues in contact with LEU 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B MET* 3.8 21.2 - - - +
80B ALA* 4.1 11.0 - - + -
83B PHE* 4.7 6.1 - - + -
84B VAL* 3.8 17.7 - - + -
117B LYS 2.8 17.4 + - - +
118B VAL* 3.2 5.8 + - - +
120B LYS* 1.3 77.3 - - - +
122B PHE* 1.3 62.5 + - - +
124B SER* 3.2 5.4 + - - -
125B VAL* 3.0 37.8 + - + +
247B MET* 4.6 2.5 - - + -
249B LEU* 3.7 39.9 - - + -
269B PHE* 4.9 2.7 - - + -
273B PHE* 4.0 20.6 - - + -
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Residues in contact with PHE 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B VAL* 2.9 39.8 + - + -
119B GLY* 3.6 7.6 - - - +
121B LEU* 1.3 77.9 - - - +
123B ALA* 1.3 62.4 + - - +
125B VAL 3.4 0.3 + - - -
126B PHE* 3.0 36.6 + + + +
144B LEU* 4.4 8.5 - - + -
148B ALA* 4.1 16.4 - - + -
152B LEU* 5.0 1.3 - - - -
200B LEU* 5.4 0.7 - - + -
202B ILE* 3.8 36.6 - - + -
230B GLY* 3.7 29.6 - - - -
231B VAL 3.8 19.3 - - - -
232B LEU* 4.0 2.7 - - - -
247B MET* 3.1 31.2 - - + -
249B LEU* 4.4 7.9 - - + -
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Residues in contact with ALA 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B HIS* 4.9 0.8 + - - +
73B PRO* 4.5 9.0 - - + +
119B GLY 2.9 16.2 + - - +
120B LYS 3.8 3.1 - - - +
122B PHE* 1.3 73.2 - - - +
124B SER* 1.3 57.3 + - - +
127B ALA* 2.9 32.7 + - - +
148B ALA* 4.2 0.6 - - - +
151B TYR* 3.4 34.3 - - + -
152B LEU* 3.7 31.7 - - + +
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Residues in contact with SER 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B PRO 4.0 10.7 + - - -
74B LYS* 2.9 36.9 + - - +
75B MET* 2.8 42.4 + - - -
120B LYS 2.7 20.8 + - - -
121B LEU* 3.4 7.6 - - - -
122B PHE 3.2 0.2 - - - -
123B ALA* 1.3 77.2 - - - +
125B VAL* 1.3 65.0 + - - +
127B ALA* 3.4 6.0 + - - +
273B PHE* 5.0 3.6 - - - -
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Residues in contact with VAL 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B LYS* 5.2 0.2 - - - +
121B LEU* 3.0 19.4 + - + +
122B PHE 4.0 2.7 - - - +
124B SER* 1.3 79.6 - - - +
126B PHE* 1.3 73.8 + - + +
127B ALA 3.3 2.5 + - - -
128B GLU* 4.4 7.6 + - - +
129B ARG* 5.2 4.8 + - - +
247B MET* 3.5 29.2 - - + -
272B PHE* 3.5 49.4 - - + +
273B PHE* 3.9 24.2 - - + -
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Residues in contact with PHE 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B PHE* 3.0 32.8 + + + +
123B ALA 3.6 2.5 - - - +
125B VAL* 1.3 87.5 - - + +
127B ALA* 1.3 63.4 + - - +
128B GLU 3.2 4.6 + - - -
129B ARG* 3.3 56.5 + - + +
131B ILE* 3.5 29.2 - - + +
152B LEU* 4.4 3.9 - - + +
200B LEU* 3.8 27.8 - - + -
202B ILE* 5.0 0.2 - - + -
227B ALA 4.9 0.2 - - - -
228B GLY* 4.0 9.2 - - - -
229B ILE 3.5 29.6 - - - -
245B GLU* 4.9 0.9 - - - -
247B MET* 4.2 26.2 - - + -
272B PHE* 4.6 3.4 - + - -
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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