Contacts of the strand formed by residues 98 - 106 (chain E) 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 E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90E GLU 5.1 0.5 - - - +
91E VAL* 3.7 8.1 + - - +
94E THR* 4.4 7.8 + - - +
96E SER* 2.7 28.4 + - - -
97E LEU* 1.3 80.0 - - - +
99E ALA* 1.3 64.3 + - - +
120E GLN* 4.3 9.9 - - - -
121E VAL 3.2 7.6 - - - -
122E SER* 3.5 11.4 - - - -
201E FMT 3.4 22.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 99 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90E GLU* 4.0 18.4 - - + +
91E VAL* 4.2 4.7 - - + +
98E SER* 1.3 77.9 - - - +
100E SER* 1.3 62.0 + - - +
101E PHE* 3.8 26.3 - - + -
120E GLN* 3.5 5.8 + - - +
121E VAL 2.9 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 100 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99E ALA* 1.3 75.0 - - - +
101E PHE* 1.3 73.3 + - - +
118E VAL* 6.2 2.0 - - - -
119E LEU 3.4 9.4 - - - -
120E GLN* 4.1 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 101 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86E VAL* 3.5 44.0 - - + -
87E PRO* 4.9 0.9 - - + -
90E GLU* 3.6 36.1 - - + -
91E VAL* 4.0 14.8 - - + -
99E ALA* 3.8 35.0 - - + -
100E SER* 1.3 80.2 - - - +
102E ASN* 1.3 59.0 + - - +
103E ALA* 3.6 7.4 - - + +
117E LEU 3.3 1.6 - - - +
118E VAL* 3.3 6.5 - - - +
119E LEU* 2.7 52.4 + - + +
121E VAL* 4.1 12.1 - - + -
93F ALA 6.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 102 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E TYR* 5.5 1.4 + - - -
10E GLU* 5.9 2.2 + - - -
100E SER 4.3 0.2 - - - -
101E PHE* 1.3 70.6 - - - +
103E ALA* 1.3 58.9 + - - +
116E SER* 3.6 11.9 + - - -
117E LEU 3.5 2.0 - - - +
118E VAL* 3.3 27.2 - - + +
93F ALA 3.4 15.7 + - - +
94F THR* 3.6 2.8 - - + -
95F PRO* 3.2 47.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 103 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84E ALA* 4.1 23.1 - - + -
86E VAL* 5.1 5.6 - - + -
101E PHE* 4.7 12.6 - - + -
102E ASN* 1.3 72.0 - - - +
104E PRO* 1.3 68.7 - - + +
105E LEU* 3.5 0.5 + - - +
116E SER* 3.2 2.6 - - - -
117E LEU* 2.7 44.9 + - + +
119E LEU* 4.8 5.2 - - + -
206E FMT 4.3 8.5 - - - +
92F LEU 5.6 0.2 - - - +
93F ALA 4.6 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 104 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83E GLU 4.3 0.9 - - - +
84E ALA* 4.5 0.7 - - - +
102E ASN 3.6 8.3 - - - +
103E ALA* 1.3 83.2 - - + +
105E LEU* 1.3 65.0 + - - +
106E LEU* 3.8 5.9 + - + +
112E PRO* 5.3 5.2 - - + -
115E ALA 3.6 8.3 - - - +
116E SER* 4.2 4.7 - - - -
206E FMT 3.0 24.2 + - - +
92F LEU* 3.2 35.2 - - + +
93F ALA 4.1 0.4 - - - -
94F THR 3.7 20.2 - - - +
95F PRO* 4.4 4.9 - - + -
97F LEU* 3.8 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 105 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E ALA* 5.1 3.1 - - + -
12E VAL* 5.1 2.2 - - + -
67E VAL 5.2 0.7 - - - +
69E VAL* 3.7 33.9 - - + -
81E LEU* 5.6 0.9 - - + -
82E GLY* 4.0 15.0 - - - +
83E GLU* 3.7 10.3 - - - +
84E ALA* 4.0 20.2 - - + +
103E ALA 4.3 0.7 - - - +
104E PRO* 1.3 73.3 - - - +
106E LEU* 1.3 61.0 + - - +
112E PRO* 3.4 5.7 - - - +
113E THR* 2.9 33.8 + - - +
115E ALA* 2.9 38.3 + - + +
116E SER* 4.1 11.4 - - - +
117E LEU* 3.8 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 106 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80E PHE* 3.8 0.2 - - - -
82E GLY* 3.3 4.7 - - - -
83E GLU* 2.9 44.8 + - + +
104E PRO* 4.4 10.1 - - + +
105E LEU* 1.3 76.2 - - - +
107E ASP* 1.3 68.6 + - - +
110E LYS* 3.8 35.7 - - + +
111E GLN 3.3 2.2 - - - +
112E PRO* 3.7 28.0 - - + -
113E THR* 3.8 3.4 - - - -
206E FMT 4.4 14.8 - - - +
60F ASP* 4.4 11.7 - - + +
92F LEU* 4.0 29.4 - - + -
----------------------------------------------------------
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