Contacts of the strand formed by residues 98 - 106 (chain F) in PDB entry 4IHB
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 98 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90F GLU 4.1 7.3 - - - +
91F VAL* 3.6 7.6 + - - +
94F THR* 4.7 2.4 + - - -
96F SER* 3.3 25.8 + - - -
97F LEU* 1.3 80.8 - - - +
99F ALA* 1.3 63.9 + - - +
120F GLN* 3.7 12.8 + - - -
121F VAL 3.2 7.4 - - - -
122F SER* 3.5 19.1 - - - +
202F FMT 4.7 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 99 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90F GLU* 3.7 30.3 - - + +
91F VAL* 4.2 3.4 - - + -
98F SER* 1.3 79.3 - - - +
100F SER* 1.3 59.3 + - - +
101F PHE* 3.8 18.1 - - + -
120F GLN* 3.6 5.9 - - - +
121F VAL* 2.7 34.9 + - - +
202F FMT 3.3 17.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 100 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90F GLU* 3.6 6.4 - - - +
99F ALA* 1.3 73.5 - - - +
101F PHE* 1.3 71.6 + - - +
118F VAL* 6.1 0.2 - - - -
119F LEU 3.4 11.0 - - - -
120F GLN* 4.1 12.3 - - - +
201F FMT 3.0 23.0 + - - -
202F FMT 3.1 33.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 101 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86F VAL* 3.5 34.3 - - + -
87F PRO* 3.6 28.9 - - + -
88F LEU* 5.1 0.9 - - + -
90F GLU* 3.5 34.8 - - + -
91F VAL* 4.8 4.9 - - + -
99F ALA* 3.8 24.2 - - + -
100F SER* 1.3 77.9 - - - +
102F ASN* 1.3 60.6 + - - +
103F ALA* 3.8 7.0 - - + +
117F LEU 3.4 1.2 - - - +
118F VAL* 3.3 5.9 - - - +
119F LEU* 2.8 54.4 + - + +
121F VAL* 4.2 18.8 - - + -
201F FMT 4.2 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 102 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D ALA 3.2 18.8 + - - +
95D PRO* 3.3 39.9 - - + +
8F TYR* 5.2 1.8 + - - -
10F GLU* 5.7 3.4 + - - +
101F PHE* 1.3 71.3 - - - +
103F ALA* 1.3 59.9 + - - +
116F SER* 3.5 16.3 + - - -
117F LEU 3.5 2.9 - - - +
118F VAL* 3.5 24.4 - - + +
201F FMT 4.1 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 103 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D LEU 5.5 1.1 - - - +
93D ALA* 4.4 3.4 - - - +
67F VAL* 5.9 0.4 - - + -
84F ALA* 4.0 23.3 - - + -
85F LYS 5.8 1.6 - - - +
86F VAL* 5.3 6.1 - - + -
101F PHE* 5.0 9.0 - - + -
102F ASN* 1.3 73.6 + - - +
104F PRO* 1.3 70.3 - - + +
105F LEU* 3.5 1.0 + - - +
116F SER* 3.2 3.0 - - - -
117F LEU* 2.7 44.2 + - + +
119F LEU* 5.1 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 104 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D LEU* 3.1 33.0 - - + +
93D ALA 3.8 0.2 - - - -
94D THR 3.2 35.0 - - - +
95D PRO* 4.3 5.6 - - + +
97D LEU* 3.7 24.0 - - + -
83F GLU 4.0 0.3 - - - +
84F ALA* 3.9 12.5 - - - +
103F ALA* 1.3 84.1 - - + +
105F LEU* 1.3 65.0 + - - +
106F LEU* 3.8 11.9 + - + +
112F PRO* 5.7 0.7 - - + -
115F ALA 3.5 9.6 - - - +
116F SER* 4.1 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 105 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F ALA* 5.0 2.9 - - + -
12F VAL* 5.7 0.7 - - + -
67F VAL* 4.9 2.2 - - + +
69F VAL* 3.6 34.3 - - + -
81F LEU* 5.8 0.4 - - + -
82F GLY* 3.7 16.8 - - - +
83F GLU* 3.5 24.7 - - - +
84F ALA* 4.2 9.2 - - + +
103F ALA 4.3 3.8 - - - +
104F PRO* 1.3 75.0 - - - +
106F LEU* 1.3 61.6 + - - +
112F PRO* 3.7 3.1 - - - +
113F THR* 2.9 32.8 + - - +
114F GLY 4.5 0.2 + - - -
115F ALA* 2.8 37.1 + - + +
116F SER 4.3 11.9 - - - +
117F LEU* 4.0 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 106 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D LEU 4.5 0.4 - - - +
92D LEU* 3.7 36.8 - - + -
80F PHE* 3.6 0.2 - - - -
82F GLY* 3.4 0.5 - - - -
83F GLU* 2.8 41.6 + - + +
84F ALA* 5.9 0.9 - - - -
104F PRO* 4.2 12.8 - - + +
105F LEU* 1.3 77.7 - - - +
107F ASP* 1.3 66.6 + - - +
110F LYS* 3.7 39.3 - - + +
111F GLN 3.6 2.5 - - - -
112F PRO* 3.6 36.1 - - + -
113F THR* 3.9 2.0 - - - -
----------------------------------------------------------
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