Contacts of the helix formed by residues 111 - 126 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107C ASP* 3.5 22.2 + - - +
108C ILE* 3.2 29.2 + - - +
109C LEU 3.6 0.4 - - - -
110C GLY* 1.3 78.3 - - - +
112C PRO* 1.3 67.8 - - + +
113C SER* 3.2 22.9 - - - +
114C VAL* 3.3 14.2 + - + +
115C LEU* 3.0 30.9 + - - +
155D PRO* 4.5 12.0 - - + +
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Residues in contact with PRO 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C GLY 3.8 2.2 - - - +
111C LYS* 1.3 87.9 - - + +
113C SER* 1.3 72.6 + - - +
115C LEU* 4.6 7.0 - - + -
116C SER* 2.9 30.1 + - - -
146D TYR* 5.7 3.8 - - + -
149D ALA* 5.0 0.9 - - + -
150D SER* 4.4 24.9 - - - +
153D ASN* 3.7 24.9 - - - +
154D VAL 3.6 35.2 - - - +
155D PRO* 4.1 2.5 - - + -
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Residues in contact with SER 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C LYS* 3.2 26.9 - - - +
112C PRO* 1.3 81.9 - - - +
114C VAL* 1.3 62.7 + - - +
116C SER* 3.8 4.3 + - - -
117C LYS* 3.5 23.0 + - - +
153D ASN* 4.9 6.1 + - - +
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Residues in contact with VAL 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C PHE* 4.3 9.6 - - + -
87C LEU* 4.0 18.6 - - + -
108C ILE* 3.9 37.9 - - + +
111C LYS* 3.3 35.7 + - + +
112C PRO 3.2 0.4 - - - -
113C SER* 1.3 79.1 - - - +
115C LEU* 1.3 65.9 + - + +
117C LYS* 3.1 7.4 + - - +
118C VAL* 3.0 32.8 + - + +
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Residues in contact with LEU 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C ILE* 4.3 4.9 - - + +
109C LEU* 3.4 24.9 - - + +
111C LYS 3.0 20.7 + - - +
112C PRO* 4.0 4.5 - - + +
114C VAL* 1.3 75.0 - - + +
116C SER* 1.3 60.8 + - - +
118C VAL* 3.9 4.6 - - + +
119C GLY 2.8 27.2 + - - -
143C PRO* 3.9 6.3 - - + +
144C LEU* 3.9 41.0 - - + +
147C ALA* 3.5 17.2 - - + +
146D TYR* 2.9 42.6 - - + -
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Residues in contact with SER 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C PRO 2.9 20.3 + - - -
113C SER* 4.0 5.2 - - - -
115C LEU* 1.3 75.0 - - - +
117C LYS* 1.3 58.9 + - - +
120C LYS* 3.0 26.3 + - - +
147C ALA* 4.8 2.9 - - - +
151C TYR* 2.7 36.3 + - - -
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Residues in contact with LYS 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C MET* 3.5 20.3 - - + +
79C GLU* 2.9 29.2 + - - +
83C PHE* 3.5 41.7 - - + -
113C SER 3.5 13.7 + - - +
114C VAL 3.1 3.7 + - - +
116C SER* 1.3 76.0 - - - +
118C VAL* 1.3 59.6 + - - +
120C LYS* 3.3 5.7 + - + +
121C LEU* 2.9 28.1 + - - +
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Residues in contact with VAL 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C PHE* 3.6 23.8 - - + -
114C VAL* 3.0 28.7 + - + +
115C LEU* 3.9 3.8 - - + +
117C LYS* 1.3 75.0 - - - +
119C GLY* 1.3 63.0 + - - +
121C LEU* 3.4 5.6 + - - +
122C PHE* 3.0 37.8 + - + -
144C LEU* 3.1 33.4 - - + -
232C LEU* 4.1 21.1 - - + -
249C LEU* 4.1 13.2 - - + -
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Residues in contact with GLY 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C LEU 2.8 16.9 + - - -
116C SER 3.9 0.9 - - - -
118C VAL* 1.3 79.3 - - - +
120C LYS* 1.3 56.0 + - - +
122C PHE* 3.4 3.9 + - - +
123C ALA* 2.8 30.1 + - - +
144C LEU* 4.9 1.5 - - - +
147C ALA* 4.0 5.4 - - - +
148C ALA* 3.7 29.3 - - - -
151C TYR* 3.8 6.5 - - - -
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Residues in contact with LYS 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C GLY 2.8 27.7 + - - -
56C ILE* 3.3 18.3 + - - +
71C TYR* 5.2 0.4 - - - -
73C PRO* 4.5 7.4 - - + -
74C LYS 3.1 26.3 + - - +
75C MET* 3.9 16.8 - - + +
79C GLU* 4.4 9.4 + - - +
116C SER 3.0 19.4 + - - +
117C LYS* 3.7 8.7 - - + +
119C GLY* 1.3 72.6 - - - +
121C LEU* 1.3 55.2 + - - +
123C ALA* 3.5 0.9 - - - +
124C SER* 2.6 37.6 + - - -
151C TYR* 3.6 36.2 - - + +
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Residues in contact with LEU 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C MET* 3.7 17.9 - - + +
80C ALA* 3.8 24.0 - - + -
83C PHE* 4.8 4.9 - - + -
84C VAL* 4.0 16.2 - - + -
117C LYS 2.9 18.0 + - - +
118C VAL* 3.7 6.1 - - - +
120C LYS* 1.3 76.3 - - - +
122C PHE* 1.3 55.4 + - - +
124C SER* 3.2 3.1 + - - -
125C VAL* 2.9 31.9 + - + +
247C MET* 5.1 1.3 - - + -
249C LEU* 3.8 33.4 - - + -
269C PHE* 4.7 3.1 - - + -
273C PHE* 3.2 37.5 - - + -
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Residues in contact with PHE 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C VAL* 3.0 37.7 + - + -
119C GLY 3.6 6.3 - - - +
121C LEU* 1.3 74.3 - - - +
123C ALA* 1.3 65.0 + - - +
125C VAL 3.3 0.3 + - - -
126C PHE* 3.0 40.1 + + + +
144C LEU* 4.2 7.9 - - + -
148C ALA* 4.1 15.9 - - + -
152C LEU* 5.3 1.1 - - - -
200C LEU* 5.1 0.9 - - + -
202C ILE* 3.6 36.8 - - + -
230C GLY* 3.7 11.9 - - - -
231C VAL 3.7 31.9 - - - -
232C LEU 4.1 1.3 - - - -
247C MET* 3.4 30.3 - - + -
249C LEU* 4.2 17.3 - - + -
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Residues in contact with ALA 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C HIS* 5.1 1.2 + - - +
73C PRO* 4.7 7.0 - - + +
119C GLY 2.8 22.3 + - - +
120C LYS* 3.6 3.6 - - - +
122C PHE* 1.3 73.3 - - - +
124C SER* 1.3 58.1 + - - +
126C PHE 3.6 0.3 - - - -
127C ALA* 2.9 33.3 + - - +
148C ALA* 4.1 4.7 - - - +
151C TYR* 3.3 29.4 - - + -
152C LEU* 3.6 27.6 - - + +
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Residues in contact with SER 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C PRO 4.0 10.3 + - - -
74C LYS* 2.9 39.3 + - - +
75C MET* 2.8 42.9 + - - -
120C LYS 2.6 22.3 + - - -
121C LEU* 3.4 6.7 - - - -
123C ALA* 1.3 73.6 - - - +
125C VAL* 1.3 64.7 + - - +
127C ALA* 3.4 6.8 + - - +
273C PHE* 4.9 3.8 - - - -
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Residues in contact with VAL 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C LYS* 5.1 0.4 + - - +
121C LEU* 2.9 20.5 + - + +
122C PHE 3.3 1.1 + - - +
124C SER* 1.3 74.4 - - - +
126C PHE* 1.3 70.2 + - + +
127C ALA 3.5 0.5 + - - -
128C GLU* 4.9 1.7 + - - +
129C ARG* 5.1 5.5 + - - +
247C MET* 3.6 31.4 - - + -
272C PHE* 3.6 44.9 - - + +
273C PHE* 3.7 33.0 - - + -
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Residues in contact with PHE 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C PHE* 3.0 34.4 + + - +
123C ALA* 3.6 2.5 - - - -
125C VAL* 1.3 83.3 - - + +
127C ALA* 1.3 63.7 + - - +
128C GLU 3.0 4.7 + - - -
129C ARG* 3.1 48.9 + - + +
131C ILE* 3.7 28.5 - - + +
152C LEU* 4.8 1.4 - - - +
200C LEU* 3.7 25.4 - - + -
227C ALA 5.3 0.4 - - - -
228C GLY* 3.8 21.3 - - - -
229C ILE 3.5 26.2 - - - -
230C GLY* 4.3 2.5 - - - -
245C GLU* 5.1 0.9 - - - -
247C MET* 3.9 30.3 - - + -
272C PHE* 4.5 4.9 - + - -
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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