Contacts of the helix formed by residues 99 - 104 (chain 2) in PDB entry 3EXG
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 LYS 99 (chain 2).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
942 ILE* 3.4 20.5 + - + +
952 ASN* 3.1 31.3 + - - +
972 ALA 3.2 0.8 - - - -
982 ALA* 1.3 80.5 - - + +
1002 THR* 1.3 60.2 + - - +
1012 TYR 3.4 0.7 - - - -
1022 TYR* 3.3 5.9 + - - +
1032 MET* 2.9 40.4 + - + +
1402 PRO 5.2 2.5 - - - +
84Z ASN* 5.1 0.8 + - - -
126Z ALA* 3.1 35.0 + - + +
127Z GLN* 4.5 3.4 - - + +
130Z GLN* 3.0 31.9 + - - +
266Z TRP* 3.8 23.5 - - - -
301Z PRO* 4.1 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 100 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1271 TYR* 3.9 20.7 + - + +
712 MET* 4.2 6.5 - - + +
952 ASN 4.1 4.0 + - - -
962 SER* 2.9 29.0 + - - -
972 ALA 3.4 4.0 + - - -
992 LYS* 1.3 75.8 - - - +
1012 TYR* 1.3 67.5 + - - +
1032 MET* 4.0 8.8 - - - +
1042 SER* 2.9 21.5 + - - -
1082 GLN* 3.3 37.7 - - + +
1102 VAL* 3.9 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 101 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3381 HIS* 3.3 21.5 - - - +
3391 ILE 4.1 9.0 - - - +
3401 TYR* 3.4 31.6 - - - -
3411 SER* 3.4 23.8 + - - +
3421 SER 5.0 0.5 + - - -
3611 SER 3.1 22.0 + - - -
972 ALA 4.6 2.6 + - - -
982 ALA 4.6 2.2 + - - +
992 LYS 3.4 0.2 - - - -
1002 THR* 1.3 78.7 - - - +
1022 TYR* 1.3 62.9 + - - +
1042 SER* 3.0 5.1 + - - -
1062 GLY* 3.0 61.3 + - - -
1082 GLN 3.4 25.9 + - - +
1092 PRO* 3.5 17.3 - - + -
1102 VAL* 4.8 2.6 - - + +
1652 ASN* 5.5 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 102 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1201 LYS* 3.8 25.0 + - + +
3351 LEU* 2.9 29.0 + - - +
3371 TYR 3.5 22.2 - - - -
3381 HIS* 3.1 16.4 + - - +
3391 ILE* 4.1 13.4 + - + +
982 ALA 5.2 1.3 + - - +
992 LYS 3.3 3.9 + - - +
1002 THR 3.2 0.8 - - - -
1012 TYR* 1.3 79.1 - - - +
1032 MET* 1.3 67.3 + - + +
1052 GLY* 3.1 14.2 + - - -
300Z VAL* 4.3 9.3 - - + +
301Z PRO* 3.1 63.1 + - + -
302Z MET 4.3 1.3 - - - -
303Z PRO* 3.3 37.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 103 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1171 ALA* 3.8 8.5 - - - +
1201 LYS* 4.3 4.4 - - - +
1211 GLY* 3.8 24.8 + - - -
1251 HIS* 3.5 55.9 - - + +
1271 TYR* 3.8 17.3 - - + +
1351 ASN* 6.2 0.4 - - - -
952 ASN 4.1 10.3 - - - +
992 LYS* 2.9 25.6 + - - +
1002 THR* 4.0 7.0 - - - +
1022 TYR* 1.3 77.0 - - + +
1042 SER* 1.3 58.8 + - - +
1052 GLY* 3.2 3.6 + - - -
125Z ALA* 5.9 0.2 - - + -
126Z ALA* 3.9 24.0 - - + +
127Z GLN* 3.7 29.2 - - - +
302Z MET 5.6 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 104 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1161 CYS 4.7 0.3 - - - +
1171 ALA* 4.3 8.6 - - - +
1271 TYR* 3.5 32.0 - - - +
1002 THR 2.9 15.6 + - - -
1012 TYR 3.0 13.9 + - - -
1032 MET* 1.3 76.6 - - - +
1052 GLY* 1.3 60.7 + - - +
1072 LEU* 3.1 22.8 + - - +
1082 GLN* 3.0 35.4 + - - +
----------------------------------------------------------
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