Contacts of the strand formed by residues 112 - 125 (chain D) 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 PRO 112 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D PRO* 5.7 0.4 - - + -
105D LEU 4.0 0.4 - - - +
106D LEU* 3.8 12.3 - - + -
107D ASP* 3.8 7.3 - - - +
111D GLN* 1.3 93.5 - - + +
113D THR* 1.3 59.5 + - - +
114D GLY 4.4 0.2 - - - +
0E PHE* 3.0 32.1 - - + -
54E LEU* 5.1 0.4 - - + -
59E LEU* 5.4 0.4 - - + -
92E LEU* 3.6 28.5 - - + -
97E LEU* 3.8 28.0 - - + -
123E TYR* 3.9 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 113 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D ASN 5.2 1.7 - - - +
13D HIS* 6.2 0.2 - - - +
81D LEU 3.8 20.1 + - - +
82D GLY* 4.5 0.2 - - - -
104D PRO* 6.2 0.2 - - - +
105D LEU* 2.7 27.9 + - - +
106D LEU 3.7 2.7 - - - -
107D ASP* 3.6 29.6 - - + +
112D PRO* 1.3 74.6 - - - +
114D GLY* 1.3 57.2 + - - +
115D ALA* 3.1 26.4 + - - +
0E PHE* 4.1 8.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 114 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D ASN* 3.5 20.0 - - - +
112D PRO* 3.6 3.6 - - - +
113D THR* 1.3 78.4 - - - +
115D ALA* 1.3 61.4 + - - +
116D SER* 5.3 1.0 + - - -
0E PHE* 4.0 11.9 - - - -
95E PRO 5.5 2.6 - - - +
97E LEU* 4.8 11.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 115 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D ASN* 3.3 29.6 - - - +
12D VAL* 4.0 8.5 - - + +
13D HIS 5.1 0.4 - - - +
104D PRO* 3.4 5.9 - - - +
105D LEU* 2.7 45.1 + - + +
113D THR* 3.1 17.7 + - - +
114D GLY* 1.3 82.0 + - - +
116D SER* 1.3 57.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 116 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D ALA* 3.2 8.1 - - - +
10D GLU* 3.0 53.2 + - - +
11D ASN 4.3 4.4 - - - +
102D ASN* 3.6 12.5 + - - -
103D ALA 3.1 16.8 - - - -
104D PRO* 4.2 1.3 - - - -
105D LEU* 4.1 5.5 - - - +
114D GLY 4.1 1.7 + - - -
115D ALA* 1.3 76.8 - - - +
117D LEU* 1.3 60.5 + - - +
95E PRO* 4.0 19.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 117 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D ILE* 4.1 11.9 - - + -
8D TYR 3.6 15.0 - - - +
9D ALA* 4.0 4.9 - - + -
24D CYS* 4.3 3.4 - - - -
46D TRP* 3.6 26.5 - - + -
67D VAL* 3.4 33.7 - - + -
69D VAL* 4.2 10.1 - - + -
84D ALA* 5.8 3.1 - - + -
101D PHE 3.4 2.9 - - - +
103D ALA* 2.8 40.7 + - + +
105D LEU* 4.2 15.7 - - + -
116D SER* 1.3 75.1 - - - +
118D VAL* 1.3 66.5 + - - +
119D LEU* 3.8 28.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 118 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D ILE* 4.1 0.7 - - - -
7D LEU* 3.0 44.0 + - + +
8D TYR* 2.8 59.0 + - + +
10D GLU* 4.7 2.2 - - + +
100D SER* 6.1 1.8 - - - -
101D PHE 3.2 8.5 - - - +
102D ASN* 3.3 31.2 - - - +
117D LEU* 1.3 73.7 - - - +
119D LEU* 1.3 67.0 + - - +
212D FMT 3.9 15.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 119 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D VAL* 4.3 5.8 - - + -
5D PHE 3.1 16.4 - - - +
6D ILE* 4.4 9.4 - - + -
7D LEU* 4.8 2.2 - - - -
65D LEU* 3.7 30.3 - - + -
67D VAL* 4.4 9.0 - - + -
84D ALA* 6.2 0.2 - - + -
86D VAL* 4.1 16.8 - - + -
100D SER* 3.5 3.0 - - - -
101D PHE* 2.7 59.5 + - + +
103D ALA* 4.8 5.4 - - + -
117D LEU* 3.8 28.3 - - + +
118D VAL* 1.3 78.8 - - - +
120D GLN* 1.3 58.5 + - - +
121D VAL* 4.0 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 120 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D ARG* 4.2 0.5 + - - +
4D VAL* 3.4 2.8 - - - +
5D PHE* 2.8 65.8 + - + +
7D LEU* 5.0 7.9 - - + +
98D SER* 4.3 12.9 + - - -
99D ALA 3.5 13.2 + - - +
100D SER* 4.0 12.7 - - - +
119D LEU* 1.3 74.3 - - - +
121D VAL* 1.3 84.5 + - - +
122D SER* 3.6 9.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 121 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D LEU* 3.6 28.5 - - + -
3D ARG 3.3 7.2 - - - +
4D VAL* 3.9 17.0 - - + -
65D LEU* 4.1 6.3 - - + -
86D VAL* 4.8 2.5 - - + -
88D LEU* 4.2 6.5 - - + -
91D VAL* 3.9 22.0 - - + +
98D SER* 3.2 3.6 - - - -
99D ALA 2.8 34.9 + - - +
101D PHE* 4.1 13.5 - - + -
119D LEU* 4.0 21.3 - - + -
120D GLN* 1.3 84.0 + - - +
122D SER* 1.3 64.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 122 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D MET 3.8 0.3 - - - +
2D LEU* 3.7 8.8 - - - +
3D ARG* 2.8 73.6 + - - +
91D VAL* 4.7 1.6 - - - -
96D SER 5.4 0.4 - - - -
97D LEU 3.4 5.4 - - - -
98D SER* 3.6 17.7 - - - -
120D GLN* 3.6 8.4 + - - -
121D VAL* 1.3 77.5 - - - +
123D TYR* 1.3 62.5 + - - +
124D THR* 3.8 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 123 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0D PHE* 3.2 34.8 - + + +
1D MET 3.7 6.7 - - - -
2D LEU* 5.0 2.0 - - - -
54D LEU* 3.4 25.8 - - + +
58D PRO* 3.9 5.9 - - - +
59D LEU* 3.2 52.1 + - + -
91D VAL* 4.1 7.2 - - + -
92D LEU* 3.5 23.6 - - + -
96D SER 5.1 0.5 - - - +
97D LEU* 2.8 40.5 + - + +
122D SER* 1.3 71.9 - - - +
124D THR* 1.3 60.3 + - - +
110F LYS 5.0 0.7 - - - -
111F GLN* 4.0 5.9 - - - +
112F PRO* 3.4 30.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 124 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0D PHE* 3.4 8.5 - - - -
1D MET* 2.8 54.2 + - + +
3D ARG* 3.7 46.5 + - + +
122D SER* 4.7 1.3 - - - -
123D TYR* 1.3 75.4 - - - +
125D ALA* 1.3 77.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 125 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-1D GLU* 3.6 16.4 - - + +
0D PHE* 4.1 14.7 - - + -
1D MET* 4.6 1.0 - - - +
124D THR* 1.3 86.7 + - - +
126D ALA* 1.3 65.5 + - - +
----------------------------------------------------------
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