Contacts of the strand formed by residues 109 - 117 (chain B) in PDB entry 5EHD
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 VAL 109 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B CYS 3.9 0.3 - - - +
22B GLU* 3.3 2.1 - - - -
23B LEU* 2.7 44.3 + - + +
47B VAL* 3.6 30.3 - - + -
48B SER 3.5 9.6 - - - +
49B LEU* 3.9 9.9 - - + -
58B HIS* 3.7 25.1 - - + -
60B VAL* 3.7 11.9 - - + -
79B LEU* 4.4 3.1 - - + -
102B LEU* 3.6 25.6 - - + -
107B GLY* 4.0 1.6 - - - -
108B PRO* 1.3 79.2 - - - +
110B HIS* 1.3 66.4 + - - +
111B ILE* 4.1 3.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ILE* 5.4 1.8 - - + -
75A THR* 3.3 41.2 + - + +
103A LYS* 3.4 26.7 + - + -
21B CYS 3.3 7.9 - - - +
22B GLU* 3.2 40.3 + - + -
46B THR 3.9 0.3 - - - +
47B VAL* 3.4 6.2 - - - +
48B SER* 2.8 36.2 + - - +
49B LEU 4.4 0.2 - - - -
50B GLY* 3.5 33.3 + - - -
51B ALA 5.0 0.7 - - - -
108B PRO* 4.6 5.4 - - + -
109B VAL* 1.3 73.4 - - - +
111B ILE* 1.3 65.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A VAL* 5.0 0.7 - - - +
75A THR 4.9 1.8 + - - +
19B PHE* 4.3 6.3 - - + -
20B GLY* 3.1 5.5 - - - -
21B CYS* 2.8 50.5 + - - +
23B LEU* 4.2 16.2 - - + -
44B LEU* 3.7 32.8 - - + -
46B THR 3.5 5.2 - - - +
47B VAL* 3.5 39.3 - - + -
60B VAL* 3.9 18.8 - - + -
76B LEU* 5.5 3.4 - - + -
100B LEU* 4.5 8.7 - - + -
109B VAL* 4.7 1.3 - - + +
110B HIS* 1.3 78.5 - - - +
112B SER* 1.3 66.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A VAL* 3.4 18.2 - - - -
75A THR 3.3 22.8 + - - -
76A LEU* 4.5 0.5 - - - -
92A PHE* 3.6 15.1 - - - -
19B PHE* 3.6 6.5 - - - -
20B GLY* 4.4 0.2 - - - -
44B LEU* 3.7 3.3 - - - -
45B ARG 2.7 28.1 + - - -
46B THR* 2.4 39.5 + - - +
111B ILE* 1.3 78.5 - - - +
113B GLY* 1.3 53.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A PHE* 3.6 11.9 - - - -
18B LEU* 3.7 2.4 - - - +
19B PHE* 2.8 40.4 + - - +
43B SER 3.0 14.6 - - - -
44B LEU* 4.2 0.9 - - - -
45B ARG* 3.8 10.3 - - - -
112B SER* 1.3 77.8 - - - +
114B GLN* 1.3 60.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A PHE* 3.7 14.1 - - + -
93A GLU* 3.4 44.3 + - - +
16B ASN* 3.6 15.9 - - + +
17B TYR 3.3 8.5 - - - +
18B LEU* 5.7 0.7 - - + -
19B PHE* 4.1 4.3 - - - -
41B GLN 3.7 0.2 - - - +
42B LEU* 3.6 6.8 - - - +
43B SER* 2.7 40.3 + - - +
45B ARG* 3.2 30.7 - - - +
113B GLY* 1.3 78.0 - - - -
115B HIS* 1.3 59.5 + - - +
116B LEU* 3.6 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A TYR* 3.5 40.8 - + + +
68A GLU* 4.7 4.9 + - - -
16B ASN* 3.3 3.1 - - - -
17B TYR* 2.7 50.9 + - + +
18B LEU 4.8 1.6 - - - +
19B PHE* 4.1 13.1 - - + +
31B PHE* 3.5 35.8 - + + -
32B LYS* 5.3 3.1 - - + +
33B VAL* 5.6 0.9 - - + -
40B HIS* 2.9 31.4 + + + -
41B GLN 3.6 5.4 - - - -
42B LEU* 5.0 0.9 - - - -
114B GLN* 1.3 71.7 - - - +
116B LEU* 1.3 73.5 + - - +
117B VAL* 3.9 6.9 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
14B PRO* 5.6 7.9 - - + +
15B GLN 3.3 5.2 - - - +
16B ASN* 3.5 28.0 - - + -
39B GLU 3.6 0.4 - - - +
40B HIS* 3.3 7.4 - - - -
41B GLN* 2.8 53.8 + - + +
43B SER* 3.9 24.5 - - - +
93B GLU* 5.1 8.1 - - + +
114B GLN* 3.6 17.7 - - + +
115B HIS* 1.3 72.2 - - - +
117B VAL* 1.3 65.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A TYR* 3.9 20.9 - - + +
14B PRO* 3.7 6.0 - - - +
15B GLN* 2.9 39.0 + - + +
17B TYR* 3.9 24.2 - - + +
38B ASN* 3.7 28.5 - - + +
39B GLU 3.4 4.7 - - - +
40B HIS* 4.1 9.4 - - - +
115B HIS* 3.9 18.2 - - + +
116B LEU* 1.3 80.5 - - - +
118B ALA* 1.3 67.4 + - - +
----------------------------------------------------------
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