Contacts of the helix formed by residues 127 - 139 (chain I) in PDB entry 3J7Y
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 PRO 127 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2216A A 3.6 33.4 - - - +
2217A C 3.5 18.8 - - - +
82I LEU* 6.4 1.8 - - + -
125I VAL 4.8 0.7 - - - +
126I PHE* 1.4 87.0 - - + +
128I ASN* 1.3 54.0 + - - +
129I GLN* 3.1 6.5 - - + +
130I VAL* 2.8 36.2 + - + +
131I LEU* 2.7 32.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 128 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2217A C 2.7 18.1 + - - +
2218A C 3.8 9.0 - - - +
126I PHE 3.2 2.8 + - - -
127I PRO* 1.3 70.8 - - - +
129I GLN* 1.3 56.5 + - - +
131I LEU* 3.4 6.3 - - - +
132I LYS* 2.9 28.1 + - - +
147I PHE* 3.3 29.3 - - + +
148I VAL* 3.2 31.5 + - - +
149I GLY 2.8 24.9 + - - -
151I ASN* 3.3 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 129 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2217A C 4.6 1.0 + - - +
2218A C 4.9 19.6 + - + -
127I PRO* 3.1 6.2 + - + +
128I ASN* 1.3 78.1 - - - +
130I VAL* 1.3 58.9 + - - +
132I LYS* 3.2 4.8 + - - +
133I PRO* 2.8 34.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 130 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79I ILE* 3.6 36.3 - - + +
82I LEU* 5.9 1.6 - - + -
83I ARG* 5.2 1.1 - - + -
127I PRO* 2.8 45.4 + - + +
129I GLN* 1.3 82.0 - - - +
131I LEU* 1.3 57.6 + - - +
132I LYS 3.2 0.9 + - - -
133I PRO* 3.3 12.6 - - + +
134I PHE* 2.9 71.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 131 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86I ILE* 5.1 1.3 - - + -
90I PHE* 6.2 2.7 - - + -
96I ILE* 5.9 1.3 - - + -
126I PHE* 4.6 7.0 - - + -
127I PRO 2.7 15.6 + - - +
128I ASN* 3.2 13.7 + - - +
130I VAL* 1.3 71.8 - - - +
132I LYS* 1.3 56.6 + - - +
134I PHE* 3.2 27.7 + - + +
135I LEU* 2.9 44.1 + - + +
147I PHE* 3.3 48.7 - - + -
151I ASN* 3.5 19.7 - - - +
153I LEU* 3.9 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 132 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128I ASN 2.9 12.7 + - - +
129I GLN* 3.6 6.1 - - - +
130I VAL 3.1 0.8 - - - -
131I LEU* 1.3 76.2 - - - +
133I PRO* 1.4 71.6 - - + +
135I LEU* 3.2 13.4 + - - +
136I GLU* 2.9 31.2 + - + +
144I LEU* 2.7 51.0 + - + +
147I PHE* 5.4 10.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 133 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83I ARG* 5.2 9.7 + - + +
129I GLN* 2.8 28.7 - - + +
130I VAL* 3.3 13.7 - - + +
132I LYS* 1.4 87.5 - - + +
134I PHE* 1.3 59.7 + - + +
136I GLU* 3.2 22.1 + - + +
137I ASP* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 134 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82I LEU* 4.4 3.8 - - + -
83I ARG* 3.3 48.5 - - + +
86I ILE* 3.2 46.9 - - + -
87I ALA* 5.8 3.2 - - - +
90I PHE* 6.5 0.4 - - + -
126I PHE* 4.4 9.9 - + - -
130I VAL* 2.9 66.7 + - + -
131I LEU* 3.2 28.0 + - + +
133I PRO* 1.3 70.7 - - + +
135I LEU* 1.3 58.9 + - + +
137I ASP* 3.2 9.2 + - - +
138I SER* 2.9 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 135 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90I PHE* 4.7 12.8 - - + -
131I LEU* 2.9 31.4 + - + +
132I LYS* 3.5 7.4 - - + +
134I PHE* 1.3 75.9 - - + +
136I GLU* 1.3 58.6 + - - +
138I SER* 3.2 5.8 + - - -
139I LYS 2.9 25.1 + - - -
140I TYR* 3.4 18.1 + - + +
143I LEU* 3.5 43.7 - - + +
144I LEU* 3.4 26.0 - - + -
147I PHE* 3.3 36.8 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
132I LYS* 2.9 14.8 + - + +
133I PRO* 3.2 24.2 + - - +
135I LEU* 1.3 77.5 - - - +
137I ASP* 1.3 66.9 + - + +
139I LYS* 3.2 16.0 + - - +
140I TYR 5.5 0.9 - - - -
144I LEU* 4.4 7.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 137 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83I ARG* 4.1 34.5 + - - +
87I ALA* 4.3 15.0 - - + +
91I GLN* 5.8 0.7 + - - -
133I PRO 2.9 13.0 + - - +
134I PHE* 3.2 10.3 + - - +
136I GLU* 1.3 81.8 - - + +
138I SER* 1.3 61.8 + - - +
139I LYS* 3.5 12.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 138 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87I ALA* 4.8 11.1 + - - +
90I PHE* 4.6 24.7 - - - +
91I GLN* 6.0 0.3 + - - -
134I PHE* 2.9 17.2 + - - +
135I LEU* 3.2 6.9 + - - -
137I ASP* 1.3 77.3 + - - +
139I LYS* 1.3 68.7 + - - +
140I TYR* 3.3 27.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 139 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135I LEU 2.9 6.5 + - - -
136I GLU* 3.2 11.1 + - - +
137I ASP 3.8 11.7 - - - +
138I SER* 1.3 79.3 - - - +
140I TYR* 1.3 58.1 + - - +
141I GLN* 2.7 30.4 + - - +
----------------------------------------------------------
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