Contacts of the helix formed by residues 133 - 143 (chain I) in PDB entry 4DVQ
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 ASN 133 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108I PRO 3.9 3.5 - - - +
109I CYS* 3.4 23.7 - - - -
110I ARG* 3.1 36.4 + - - +
111I MET 5.3 0.2 - - - -
112I ILE* 4.2 17.0 - - - +
131I LEU 5.2 2.1 + - - -
132I LEU* 1.3 87.4 - - - +
134I GLY* 1.3 68.2 + - - +
135I PRO* 3.8 1.6 - - - +
136I GLU* 3.8 7.6 + - - +
137I TRP* 3.5 15.1 + - - -
448I ARG* 2.8 16.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 134 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107I HIS* 3.1 37.6 + - - +
108I PRO 4.9 3.4 + - - -
109I CYS* 5.3 2.4 - - - -
133I ASN* 1.3 76.5 + - - +
135I PRO* 1.3 72.9 - - - +
137I TRP* 3.2 4.9 + - - +
138I ARG 3.2 13.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 135 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D LEU* 5.1 4.0 - - + -
40D ALA* 4.5 16.2 - - + +
42D PRO* 5.5 8.3 - - + -
395D TYR* 4.1 19.5 - - - +
107I HIS* 3.5 24.0 - - + +
133I ASN 4.3 1.1 - - - +
134I GLY* 1.3 84.0 - - - +
136I GLU* 1.3 57.3 + - - +
138I ARG* 3.9 0.9 - - - +
139I PHE* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 136 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126I LYS* 3.5 30.3 + - - +
132I LEU* 3.2 29.6 - - + +
133I ASN 3.8 6.5 + - - +
134I GLY 3.3 0.8 - - - -
135I PRO* 1.3 77.4 - - - +
137I TRP* 1.3 65.6 + - - +
139I PHE* 3.6 10.0 - - + +
140I ASN* 2.8 42.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 137 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106I LEU 3.7 11.9 - - - -
107I HIS* 4.3 5.4 - - + -
108I PRO* 3.6 28.3 - - + -
129I VAL* 3.3 26.8 - - + +
132I LEU* 3.9 10.4 - - + +
133I ASN* 3.5 26.0 + - - +
134I GLY 3.2 12.4 + - - +
136I GLU* 1.3 76.6 - - - +
138I ARG* 1.3 98.6 + - + +
140I ASN* 2.8 6.6 + - - +
141I ARG* 2.8 34.7 + - + +
447I MET* 3.7 37.0 - - + -
448I ARG* 3.3 44.9 - - + +
601I HEM 2.9 19.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 138 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105I SER 5.2 0.2 + - - -
106I LEU* 2.7 67.2 + - - +
107I HIS* 3.6 23.1 - - + +
108I PRO* 5.2 0.6 - - - +
134I GLY 3.2 2.8 + - - +
135I PRO 4.1 0.9 - - - +
137I TRP* 1.3 104.3 - - + +
139I PHE* 1.3 66.2 + - - +
141I ARG* 4.4 2.5 - - + +
142I LEU* 3.2 51.4 + - + +
447I MET* 4.1 33.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 139 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D PHE 5.0 0.2 - - - -
73D GLN 4.1 11.7 - - - -
74D GLU 4.4 11.2 - - - -
75D LEU 4.6 5.6 - - - +
76D GLY* 3.1 39.9 - - - -
77D PRO* 3.8 3.6 - - + -
126I LYS* 5.5 4.0 - - - -
135I PRO 2.9 19.1 + - - +
136I GLU* 3.6 10.5 - - + +
138I ARG* 1.3 78.8 - - - +
140I ASN* 1.3 82.0 + - - +
142I LEU* 5.7 0.2 - - - -
143I ARG* 2.8 74.1 + - - +
298I GLU 4.9 3.8 - - - -
299I LEU* 3.7 18.8 - - + -
300I SER 6.0 0.2 - - - -
303I ALA* 6.0 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 140 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126I LYS* 5.2 5.3 + - - +
127I CYS 4.6 2.6 - - - +
129I VAL* 4.4 9.4 - - + -
132I LEU* 3.4 25.7 - - + +
136I GLU* 2.8 31.4 + - - +
137I TRP 2.8 12.0 + - - +
139I PHE* 1.3 89.5 - - - +
141I ARG* 1.3 61.4 + - - +
143I ARG* 3.1 12.5 + - - +
144I LEU* 3.4 19.3 + - + +
299I LEU* 4.1 12.6 - - - +
303I ALA* 4.1 12.7 - - - +
307I ASN* 3.3 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 141 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129I VAL* 3.9 9.8 - - + +
137I TRP* 2.8 43.1 + - + +
138I ARG* 4.1 4.3 - - + +
140I ASN* 1.3 72.9 - - - +
142I LEU* 1.3 60.3 + - + +
144I LEU* 2.9 5.1 + - - +
145I ASN* 2.9 61.8 + - - +
149I LEU* 3.5 19.6 - - - +
447I MET* 3.3 22.4 + - + +
448I ARG* 3.4 4.6 - - - +
449I GLN* 2.6 34.9 + - - +
451I LEU* 3.6 20.4 - - - +
601I HEM 3.3 34.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 142 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138I ARG* 3.2 54.8 + - + +
139I PHE 4.3 2.7 - - - +
141I ARG* 1.3 77.2 - - + +
143I ARG* 1.3 66.3 + - - +
144I LEU 3.3 0.7 - - - -
145I ASN* 4.3 17.0 - - + +
146I PRO* 3.2 23.3 - - - +
298I GLU* 5.2 0.3 - - - +
447I MET* 5.5 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 143 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D PRO* 3.3 34.4 - - - +
93D LEU* 5.8 1.0 - - - +
393D GLN* 4.9 4.0 - - - +
139I PHE* 2.8 68.8 + - - +
140I ASN 3.1 9.8 + - - +
141I ARG 3.0 1.4 - - - -
142I LEU* 1.3 92.9 - - - +
144I LEU* 1.3 58.5 + - - +
146I PRO* 4.5 6.0 - - - +
147I ASP* 5.1 1.4 - - - +
293I LEU* 3.7 17.8 - - - +
296I LYS* 6.0 1.0 - - - +
298I GLU* 3.2 40.5 + - + +
299I LEU* 3.6 28.2 - - + +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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