Contacts of the strand formed by residues 111 - 116 (chain B) in PDB entry 5IFM
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 PHE 111 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B PHE* 3.6 35.4 - + + -
78B VAL 3.2 8.7 - - - +
79B GLY* 4.1 0.9 - - - -
81B LEU* 3.6 7.9 - - - +
104B PHE* 4.0 9.4 - + - -
105B ILE* 3.8 3.7 - - - +
106B HIS* 2.9 61.2 + + + +
109B LYS* 3.4 26.7 - - + +
110B GLY* 1.3 78.9 - - - +
112B GLY* 1.3 59.3 + - - +
113B PHE* 3.6 23.3 - + - -
306C GLU 3.1 28.0 - - - -
307C HIS* 5.2 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B PHE* 3.5 4.2 - - - -
78B VAL 2.8 34.4 + - - -
81B LEU* 3.7 6.6 - - - +
90B MET* 4.4 6.7 - - - -
104B PHE* 3.0 17.5 - - - -
105B ILE* 4.2 2.5 - - - -
111B PHE* 1.3 78.6 - - - +
113B PHE* 1.3 68.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ARG* 3.5 33.9 - - - +
76B LEU 3.3 17.3 - - - +
77B PHE* 3.7 27.1 - + + -
78B VAL 4.9 0.2 - - - +
90B MET* 3.7 5.4 - - - +
102B GLU* 3.8 18.8 - - - +
103B VAL* 3.4 4.0 - - - -
104B PHE* 2.8 49.9 + + + +
111B PHE* 3.6 24.5 - + - -
112B GLY* 1.3 73.4 - - - -
114B ILE* 1.3 62.0 + - - +
144B ALA* 3.6 25.1 - - + -
145B CYS 5.4 0.9 - - - -
305C HIS 4.6 9.6 - - - -
306C GLU* 4.2 12.1 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
74B SER 3.9 0.9 - - - +
75B ARG* 3.4 2.7 - - - -
76B LEU* 2.9 41.9 + - + +
78B VAL* 4.4 3.8 - - + -
90B MET* 4.3 13.0 - - + +
91B ARG* 4.8 4.3 - - - -
94B PHE* 3.7 65.1 - - + -
100B ALA* 4.0 15.9 - - + -
102B GLU* 3.2 10.8 - - - +
103B VAL* 3.7 20.9 - - + -
113B PHE* 1.3 75.5 - - - +
115B ARG* 1.3 71.5 + - - +
116B LEU* 4.0 7.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B PHE* 2.8 44.3 + - + +
71B THR* 3.4 23.2 - - - +
72B GLN* 3.6 26.2 - - - +
74B SER 3.7 2.0 - - - -
75B ARG* 3.8 24.2 - - + +
100B ALA* 3.6 4.9 - - - -
101B GLY* 2.8 27.6 + - - -
102B GLU* 2.9 51.9 + - - +
114B ILE* 1.3 72.9 - - - +
116B LEU* 1.3 64.4 - - - +
175B GLU* 4.2 4.0 + - - -
196B SER* 4.5 9.7 + - - -
305C HIS* 4.9 7.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B PHE* 3.5 9.7 - - - -
74B SER* 2.8 37.4 + - - +
76B LEU* 4.2 9.4 - - + -
94B PHE* 4.3 14.1 - - + +
97B TYR* 4.0 16.8 - - + +
98B GLY 5.8 0.2 - - - +
99B LYS 4.2 10.8 - - - +
100B ALA* 4.8 2.7 - - + -
114B ILE* 4.2 23.6 - - + -
115B ARG* 1.3 82.1 - - - +
117B GLU* 1.3 59.1 + - - +
118B THR 3.5 1.6 - - - +
121B LEU* 3.7 16.4 - - + +
122B ALA* 3.8 17.5 - - + +
125B ALA* 3.5 32.1 - - + -
----------------------------------------------------------
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