Contacts of the strand formed by residues 107 - 115 (chain B) in PDB entry 2Y1T
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 ARG 107 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ASP* 2.7 50.1 + - + +
26B LEU 3.4 4.7 - - - -
27B ARG* 3.7 32.3 - - + +
61B ARG* 3.2 56.9 + - - +
64B THR* 4.8 0.7 + - - -
68B PHE* 4.4 7.1 - - - -
105B GLY 3.2 1.0 + - - -
106B ASP* 1.3 70.0 - - - +
108B ILE* 1.3 60.9 + - - +
68F PHE* 3.6 17.8 - - - -
101F LYS 3.7 9.5 + - - -
103F LYS* 3.5 25.5 - - - +
106F ASP* 2.9 38.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU 3.0 8.0 + - - +
28B ALA* 4.4 5.8 - - + +
42B VAL* 3.5 33.4 - - + -
44B LEU* 3.9 22.2 - - + -
60B PRO* 4.0 1.9 - - - +
61B ARG* 3.5 4.8 + - - -
64B THR* 2.6 36.7 + - + +
68B PHE* 3.7 27.4 - - + -
92B PHE* 3.7 24.9 - - + -
102B ILE* 4.0 23.1 - - + -
106B ASP* 3.2 12.1 + - + +
107B ARG* 1.3 77.7 - - - +
109B CYS* 1.3 66.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ASP* 3.4 5.0 - - - +
26B LEU* 2.9 33.2 + - - +
44B LEU* 3.7 40.2 - - - -
58B VAL* 3.8 15.9 - - + -
59B VAL 3.2 14.8 - - - +
61B ARG* 3.8 9.8 - - - +
92B PHE* 3.6 25.4 - - + -
107B ARG 3.8 0.4 - - - -
108B ILE* 1.3 78.0 - - - +
110B GLN* 1.3 62.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B TRP* 3.2 42.6 - - + +
24B ILE 3.2 9.2 - - - +
25B ASP* 3.6 20.5 - - - +
26B LEU* 4.5 1.6 - - - +
58B VAL* 3.3 6.1 - - - -
59B VAL* 2.9 46.8 + - + +
60B PRO 3.8 10.3 - - - +
61B ARG* 4.3 9.3 - - + +
62B SER 5.3 0.4 + - - -
109B CYS* 1.3 78.1 - - - +
111B PHE* 1.3 60.2 + - - +
78C VAL* 3.4 25.3 - - - +
143C DUD 4.7 13.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ILE* 4.5 10.8 - - + -
5B ILE* 6.1 0.4 - - + -
15B ILE* 5.4 0.7 - - + -
23B TRP* 3.4 9.0 - - - -
24B ILE* 2.8 83.2 + - + +
26B LEU* 3.8 21.8 - - + -
48B MET* 3.9 31.2 - - + -
50B LEU* 4.8 0.4 - - + -
56B ALA* 4.0 2.9 - - + -
57B HIS 3.1 13.5 - - - +
58B VAL* 4.1 14.8 - - + -
90B TRP* 3.9 20.6 - + + -
110B GLN* 1.3 72.8 - - - +
112B ARG* 1.3 73.8 + - - +
113B ILE* 4.3 17.3 - - + -
117C MET* 4.0 1.8 - - - +
122C LEU* 5.0 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B TRP* 3.5 46.0 - - + +
56B ALA* 3.1 4.9 - - - +
57B HIS* 2.9 33.6 + - + +
111B PHE* 1.3 81.2 - - - +
113B ILE* 1.4 87.7 + - - +
114B MET* 3.9 28.2 - - + +
55C GLU* 3.1 19.5 + - - -
57C HIS* 5.2 0.4 - - - -
114C MET* 4.1 11.7 - - - +
115C LYS 2.9 28.5 + - - -
116C LYS 4.0 0.6 + - - -
117C MET* 3.6 42.9 - - + +
118C PRO* 4.8 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 3.6 31.6 - - + -
3B ILE* 4.3 11.7 - - + -
50B LEU* 4.1 26.5 - - + -
51B PRO* 4.1 13.9 - - + -
54B TYR* 3.8 21.8 - - + -
55B GLU 3.3 11.4 - - - +
56B ALA* 4.5 1.3 - - - -
111B PHE* 4.3 6.3 - - + -
112B ARG* 1.4 104.6 + - - +
114B MET* 1.3 58.8 + - - +
117C MET* 3.5 24.5 - - + +
118C PRO* 5.0 3.2 - - + +
120C VAL* 4.4 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ARG* 4.1 7.9 - - - +
114A MET* 3.7 30.7 - - + +
23B TRP* 6.1 0.2 - - + -
54B TYR* 3.3 10.0 - - - -
55B GLU* 2.9 30.4 + - - +
57B HIS* 3.3 42.8 - - + +
112B ARG* 3.9 26.9 - - - +
113B ILE* 1.3 72.8 - - - +
115B LYS* 1.3 75.9 + - - +
57C HIS* 5.0 4.0 - - + -
114C MET* 3.7 24.9 - - + +
118C PRO* 6.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ARG* 2.9 24.1 + - - -
53B GLY* 3.7 11.4 - - - +
54B TYR* 3.5 36.0 - - + +
114B MET* 1.3 80.9 - - + +
116B LYS* 1.3 70.8 + - - +
----------------------------------------------------------
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