Contacts of the helix formed by residues 107 - 122 (chain B) in PDB entry 1YAA
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 107 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B SER* 2.9 27.7 + - - -
106B LEU* 1.3 79.8 - - - +
108B GLY* 1.3 63.2 + - - +
111B ALA* 3.3 4.7 + - - +
254B GLN 4.2 0.2 - - - +
255B SER* 4.0 2.8 + - - -
257B ALA* 4.0 7.1 + - - +
263B TYR 4.4 0.7 + - - -
266B ARG* 3.3 35.0 + - - -
267B VAL 3.4 19.8 + - - -
268B GLY* 3.6 20.3 - - - +
906B PLP 2.9 15.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B SER* 1.3 70.5 - - - +
109B THR* 1.3 61.8 + - - -
110B GLY 3.3 0.2 - - - -
111B ALA* 3.5 5.2 + - - +
112B LEU* 3.1 30.5 + - - +
222B ASP* 5.6 1.1 - - - -
253B CYS* 4.4 4.5 - - - +
254B GLN 4.2 6.3 - - - -
255B SER* 3.5 18.3 - - - -
906B PLP 2.5 31.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ARG 3.7 22.7 - - - +
293A SER 4.5 0.2 - - - -
294A GLU 3.7 13.7 - - - +
295A VAL 4.2 0.7 - - - -
296A SER* 3.5 19.7 + - - +
107B SER 3.3 0.4 - - - -
108B GLY* 1.3 73.9 - - - +
110B GLY* 1.3 60.3 + - - +
112B LEU* 3.2 9.4 + - - +
113B HIS* 2.9 26.7 + - - +
140B TRP* 3.4 18.4 - - - -
142B ASN* 3.9 1.6 - - - +
146B ILE* 3.9 19.6 - - + +
266B ARG* 4.0 2.7 - - - -
906B PLP 2.7 23.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A GLU 3.6 12.5 + - - -
295A VAL* 4.8 1.5 - - - +
105B SER* 3.9 7.2 - - - -
106B LEU* 2.9 33.2 + - - -
107B SER 4.0 0.7 - - - -
109B THR* 1.3 77.7 - - - +
111B ALA* 1.3 56.1 + - - +
113B HIS* 3.2 4.0 + - - +
114B ILE* 3.0 34.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B SER* 3.4 22.1 + - - +
107B SER 3.3 8.1 + - - +
108B GLY* 3.8 5.6 - - - +
109B THR 3.2 0.6 - - - -
110B GLY* 1.3 75.6 - - - +
112B LEU* 1.3 60.0 + - - +
114B ILE* 3.5 1.9 + - - -
115B SER* 3.0 26.9 + - - -
253B CYS* 3.6 27.1 - - + -
269B PHE* 3.4 29.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B GLY 3.1 20.6 + - - +
109B THR 3.2 4.5 + - - +
111B ALA* 1.3 75.6 - - - +
113B HIS* 1.3 58.8 + - - +
115B SER* 3.8 4.3 - - - -
116B ALA* 3.2 25.6 + - - +
140B TRP* 3.7 29.4 - - + -
143B HIS* 4.2 8.1 - - + +
146B ILE* 3.5 19.9 - - + +
147B PHE* 4.5 13.8 - - + -
187B VAL* 5.2 1.1 - - + -
220B LEU* 3.9 20.4 - - + -
222B ASP* 3.8 26.2 - - + +
253B CYS* 3.5 24.5 - - + -
906B PLP 4.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A SER 4.3 5.9 + - - +
294A GLU* 3.3 59.3 - - + +
295A VAL* 5.8 2.5 - - + -
109B THR 2.9 7.9 + - - +
110B GLY* 3.2 5.4 + - - +
112B LEU* 1.3 76.7 - - - +
114B ILE* 1.3 66.8 + - + +
115B SER 3.2 0.2 - - - -
116B ALA* 3.8 1.7 - - - -
117B LYS* 2.8 29.9 + - + +
146B ILE* 4.1 6.4 + - - -
150B GLN* 3.5 40.6 + - - +
290B ILE* 5.4 0.2 - - + -
294B GLU* 2.8 36.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B VAL* 4.4 9.2 - - + -
105B SER* 3.9 22.7 - - - -
110B GLY 3.0 21.5 + - - +
111B ALA 3.8 4.7 - - - +
113B HIS* 1.3 81.7 - - + +
115B SER* 1.3 57.3 + - - +
117B LYS* 3.5 4.9 + - - +
118B PHE* 2.9 30.8 + - - +
269B PHE* 4.5 15.9 - - + +
287B LEU* 4.0 30.1 - - + +
290B ILE* 4.5 19.3 - - + +
291B ILE* 4.1 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ALA 3.0 10.5 + - - -
112B LEU* 3.8 6.5 - - - -
113B HIS 3.2 0.4 - - - -
114B ILE* 1.3 79.8 - - - +
116B ALA* 1.3 58.2 + - - +
118B PHE* 3.3 6.1 + - - +
119B PHE* 2.8 51.6 + - - -
147B PHE* 5.1 0.9 - - - -
220B LEU* 4.0 13.3 - - - +
251B PHE* 4.0 6.6 - - - -
253B CYS* 3.7 8.0 - - - -
269B PHE* 2.8 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B LEU 3.2 15.6 + - - +
113B HIS* 3.8 4.9 - - - +
114B ILE 3.4 0.2 - - - -
115B SER* 1.3 79.2 - - - +
117B LYS* 1.3 58.4 + - - +
119B PHE* 3.4 10.3 + - - +
120B SER* 2.9 30.5 + - - -
146B ILE 3.8 13.2 - - - +
147B PHE* 3.8 19.2 - - + -
150B GLN* 3.6 20.8 - - + +
152B LEU* 3.7 6.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ASN* 3.0 51.6 + - - +
150A GLN* 3.9 12.5 + - - +
113B HIS* 2.8 22.2 + - + +
114B ILE 3.9 3.1 - - - +
116B ALA* 1.3 74.0 - - - +
118B PHE* 1.3 63.7 - - - +
120B SER* 2.9 19.8 + - - +
121B LYS* 3.2 32.5 - - + +
150B GLN* 3.2 25.9 - - - +
290B ILE* 3.9 24.5 - - + -
294B GLU* 3.8 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A PHE* 3.4 39.7 - + - -
9A ILE* 4.1 5.4 - - + -
114B ILE* 2.9 20.5 + - + +
115B SER* 3.5 6.1 - - - +
117B LYS* 1.3 77.1 - - - +
119B PHE* 1.3 67.9 + + - +
121B LYS* 3.2 3.6 + - - +
122B PHE* 3.2 61.3 + + - +
123B PHE* 4.6 3.4 - + - -
251B PHE* 4.3 19.7 - + + -
269B PHE* 5.1 2.0 - - - -
283B VAL* 3.9 28.9 - - + -
286B GLN* 4.3 8.1 - - + -
287B LEU* 3.9 21.1 - - + -
290B ILE* 4.3 13.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A PHE* 6.0 0.2 - + - -
115B SER* 2.8 38.9 + - - +
116B ALA* 3.7 8.1 - - - +
118B PHE* 1.3 84.3 - + - +
120B SER* 1.3 57.4 + - - +
123B PHE* 2.9 55.9 + + + +
147B PHE* 4.6 7.0 - + - -
152B LEU* 3.8 19.7 - - + -
185B ILE* 3.7 48.9 - - + -
218B ILE* 5.0 7.4 - - + -
220B LEU* 4.2 7.2 - - + -
251B PHE* 3.8 44.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ALA 2.9 15.1 + - - -
117B LYS* 2.9 32.1 + - - +
119B PHE* 1.3 74.5 - - - +
121B LYS* 1.3 59.1 + - - +
129B PRO* 3.4 20.4 - - - +
150B GLN* 3.3 31.8 + - - +
152B LEU* 4.1 11.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ASN* 4.7 11.4 - - - +
117B LYS* 3.2 42.4 + - + +
118B PHE 3.2 4.7 + - - +
119B PHE 3.1 0.8 - - - -
120B SER* 1.3 84.3 - - - +
122B PHE* 1.3 93.8 + - + +
129B PRO* 4.4 4.0 - - - +
286B GLN* 4.5 6.3 + - - -
290B ILE* 4.6 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ILE* 4.1 18.4 - - + -
10A GLU* 4.2 22.9 - - - -
118B PHE* 3.2 58.6 + + - +
121B LYS* 1.3 104.5 - - + +
123B PHE* 1.3 92.1 + - + +
129B PRO* 3.3 10.1 - - - +
286B GLN* 3.5 33.4 - - + -
290B ILE* 5.8 1.1 - - + -
----------------------------------------------------------
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