Contacts of the strand formed by residues 996 - 1004 (chain A) in PDB entry 1I44
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 ILE 996 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
991A VAL* 4.3 16.4 - - + -
992A SER 4.2 7.6 - - - +
993A ARG* 3.0 20.8 + - - +
994A GLU 3.3 3.6 - - - +
995A LYS* 1.3 81.8 - - + +
997A THR* 1.3 65.9 + - - +
998A LEU* 4.2 13.7 + - + +
1014A ASN 3.5 4.7 - - - +
1015A ALA* 3.7 26.2 - - + -
1018A ILE* 5.0 0.2 - - + -
1027A VAL* 5.2 0.7 - - + -
1029A VAL* 4.0 30.3 - - + -
1066A VAL* 4.8 7.4 - - + -
1073A LEU* 4.7 11.2 - - + -
1075A VAL* 4.1 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 997 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
994A GLU 5.3 0.7 + - - -
995A LYS 4.6 2.9 + - - -
996A ILE* 1.3 75.6 + - - +
998A LEU* 1.3 71.6 + - - +
999A LEU* 4.3 13.3 - - + +
1013A GLY* 2.9 4.0 - - - -
1014A ASN* 2.7 52.1 + - + +
1016A ARG* 5.0 8.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 998 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
996A ILE* 4.2 8.7 + - + +
997A THR* 1.3 84.0 - - - +
999A LEU* 1.3 63.0 + - - +
1011A TYR* 4.1 39.5 - - + -
1012A GLU 3.8 2.7 - - - +
1029A VAL* 3.7 43.1 - - + -
1031A THR* 5.4 4.5 - - + -
1073A LEU* 5.5 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 999 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
997A THR* 4.3 12.8 - - + +
998A LEU* 1.3 79.3 - - - +
1000A ARG* 1.3 69.9 + - + +
1012A GLU* 2.8 32.4 + - + +
1013A GLY* 4.1 15.5 - - - +
1014A ASN* 3.4 30.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1000 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
998A LEU* 4.0 0.4 - - - +
999A LEU* 1.3 86.1 - - + +
1001A GLU* 1.3 76.1 + - - +
1002A LEU* 3.3 21.4 - - - +
1011A TYR* 3.3 11.6 - - - +
1012A GLU* 2.8 59.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1001 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1000A ARG* 1.3 97.1 + - - +
1002A LEU* 1.3 61.7 + - - +
1003A GLY 4.8 0.4 - - - +
1009A MET* 3.2 37.7 - - + +
1010A VAL 3.9 0.2 - - - -
1011A TYR* 3.6 31.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1002 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ACP 3.5 47.6 + - + +
1000A ARG* 3.3 30.7 - - - +
1001A GLU* 1.3 74.1 - - - +
1003A GLY* 1.3 58.8 + - - +
1010A VAL* 2.8 14.9 + - + +
1011A TYR 3.7 6.5 - - - +
1012A GLU* 3.4 39.5 - - + +
1028A ALA* 4.4 2.9 - - + -
1078A LEU* 3.7 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1003 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ACP 4.0 15.2 + - - -
1001A GLU* 3.8 0.8 - - - +
1002A LEU* 1.3 82.1 - - - +
1004A GLN* 1.3 57.8 + - - -
1009A MET* 3.2 11.6 - - - +
1010A VAL* 2.7 36.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1004 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ACP 3.2 16.9 - - - +
1003A GLY* 1.3 72.5 - - - -
1005A GLY* 1.3 93.5 + - - +
1008A GLY* 3.4 15.2 + - - -
1009A MET* 3.6 31.2 + - + +
1033A ASN* 5.7 2.4 - - - +
----------------------------------------------------------
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