Contacts of the helix formed by residues 104 - 114 (chain B) in PDB entry 4A0L
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 SER 104 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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835A MET 4.9 0.9 - - - -
836A VAL* 5.6 6.1 - - - -
837A TYR 5.0 1.7 + - - -
841A ALA 2.8 6.8 + - - -
843A PRO* 2.4 47.8 - - - -
103B THR* 1.3 78.4 - - - +
105B ILE* 1.3 64.0 + - - +
106B LEU* 3.1 9.9 - - - -
107B HIS* 3.2 19.7 + - - +
108B TYR* 3.4 13.7 - - - -
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Residues in contact with ILE 105 (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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842A GLU* 4.1 20.7 - - + +
843A PRO 5.5 0.4 - - - -
885A ASN* 4.0 29.8 - - + +
909A ILE 4.9 1.1 - - - +
910A MET* 3.8 24.7 - - + -
926A LEU* 3.9 1.1 - - + -
103B THR 4.1 0.8 + - - -
104B SER* 1.3 70.6 - - - +
106B LEU* 1.3 62.3 + - - +
108B TYR* 3.1 10.5 + - - +
109B ILE* 2.9 39.3 + - + +
122B LEU* 3.7 26.0 - - + -
125B CYS* 4.2 9.7 - - - -
126B LEU* 3.5 31.6 - - + -
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Residues in contact with LEU 106 (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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814A LEU* 4.1 7.2 - - + +
834A ALA* 3.8 15.3 - - + -
843A PRO* 5.2 1.1 - - + -
869A ALA* 2.9 37.0 - - + -
885A ASN* 5.3 0.2 - - - +
104B SER* 3.1 10.0 - - - -
105B ILE* 1.3 79.7 - - - +
107B HIS* 1.3 60.1 + - - +
109B ILE* 3.8 8.9 - - - +
110B TYR* 3.0 32.8 + - - +
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Residues in contact with HIS 107 (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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812A TYR* 5.8 10.5 - - + -
836A VAL* 5.6 8.1 - - + -
101B GLY 4.5 5.8 - - - +
102B GLN* 3.8 31.4 - - + -
103B THR 4.9 0.2 - - - +
104B SER* 3.2 16.7 + - - +
106B LEU* 1.3 78.8 - - - +
108B TYR* 1.3 58.0 + - - +
110B TYR* 4.0 4.6 - - - +
111B LYS* 3.1 38.3 + - + +
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Residues in contact with TYR 108 (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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102B GLN* 3.1 50.0 + - + +
103B THR 4.6 1.1 - - - -
104B SER 3.4 24.2 - - - -
105B ILE* 3.1 7.9 + - - +
107B HIS* 1.3 77.4 - - - +
109B ILE* 1.3 64.8 + - - +
111B LYS* 4.5 2.2 - - - -
112B SER* 3.1 21.3 + - - -
118B ILE* 3.5 32.9 - - + +
121B GLN* 3.7 34.7 + - + +
122B LEU* 4.1 24.1 - - + +
124B GLN* 3.9 13.7 + - - -
125B CYS* 3.7 29.8 - - + +
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Residues in contact with ILE 109 (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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814A LEU* 5.2 7.2 - - + -
869A ALA* 5.5 4.0 - - + -
871A TYR* 4.5 18.4 - - + +
885A ASN* 5.6 6.1 - - - +
910A MET* 4.7 7.0 - - + -
912A LEU* 2.6 54.3 - - + +
913A TYR* 5.6 3.0 + - + +
926A LEU* 5.0 5.8 - - + -
105B ILE* 2.9 44.5 + - + +
106B LEU* 3.3 10.1 + - + +
108B TYR* 1.3 75.0 - - - +
110B TYR* 1.3 63.1 + - - +
112B SER* 3.0 22.5 + - - -
113B SER* 3.2 9.6 + - - -
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Residues in contact with TYR 110 (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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720A SER* 4.9 4.3 + - - -
722A ARG* 3.9 28.2 - - + +
723A LYS* 6.2 3.8 - - - -
738A SER* 3.6 17.0 + - - -
787A GLU* 3.9 21.5 - - - -
789A HIS* 4.3 11.6 - + - -
812A TYR* 4.2 19.3 - + + -
813A ALA 4.9 7.2 - - - -
814A LEU* 3.5 27.7 - - + +
106B LEU 3.0 17.1 + - - +
107B HIS* 4.1 4.9 - - - +
109B ILE* 1.3 78.2 - - - +
111B LYS* 1.3 66.0 + - + +
113B SER* 2.7 30.7 + - - -
114B LEU* 3.2 44.7 + - + +
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Residues in contact with LYS 111 (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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102B GLN* 2.9 46.4 + - + +
107B HIS* 3.1 24.6 + - + +
108B TYR* 3.9 4.7 - - - +
109B ILE 3.4 0.4 - - - -
110B TYR* 1.3 81.9 - - + +
112B SER* 1.3 61.6 + - - +
114B LEU* 3.1 14.5 + - + +
116B GLN* 2.8 57.3 + - + +
118B ILE* 4.4 15.5 - - + -
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Residues in contact with SER 112 (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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912A LEU* 4.9 4.5 - - - +
913A TYR* 4.2 14.0 + - - -
926A LEU* 5.6 2.3 - - - +
954A MET 5.7 0.2 + - - -
970A ASN* 5.9 4.0 - - - -
1003A PHE* 4.1 22.4 - - - -
108B TYR 3.1 15.4 + - - -
109B ILE* 3.0 15.9 + - - -
110B TYR 3.3 0.2 - - - -
111B LYS* 1.3 76.8 - - - +
113B SER* 1.3 57.5 + - - +
115B GLY* 3.1 16.5 + - - -
116B GLN 4.3 3.8 - - - +
117B SER 4.7 8.7 - - - +
118B ILE* 4.3 14.1 - - - +
122B LEU* 6.0 3.1 - - - -
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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
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360A VAL* 2.7 36.2 - - - +
723A LYS* 5.0 16.7 + - - -
913A TYR* 5.7 8.1 - - - -
1005A ASN* 3.9 16.5 + - - +
109B ILE* 3.2 8.9 + - - -
110B TYR* 2.7 35.4 + - - -
112B SER* 1.3 80.7 + - - +
114B LEU* 1.3 52.5 + - - +
115B GLY 3.3 1.5 + - - -
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Residues in contact with LEU 114 (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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328A LEU* 5.6 3.8 - - - +
358A PRO* 4.9 13.7 - - - +
360A VAL* 4.0 22.4 - - + -
381A ALA* 5.8 7.9 - - + -
382A PHE* 5.7 9.6 - - + -
720A SER* 5.5 9.9 - - - +
721A PRO 4.7 11.2 - - - +
722A ARG* 5.2 0.7 - - + -
787A GLU* 5.7 2.2 - - - +
1005A ASN* 5.8 0.9 - - - -
1033A VAL* 6.0 0.2 - - - -
110B TYR* 3.2 56.0 + - + +
111B LYS* 3.1 11.5 + - + +
112B SER 3.1 0.4 - - - -
113B SER* 1.3 78.2 - - - +
115B GLY* 1.3 60.8 + - - +
116B GLN* 3.5 26.9 - - - +
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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
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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