Contacts of the strand formed by residues 1026 - 1032 (chain A) in PDB entry 4UHW
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 ALA1026 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1024A GLY 4.4 0.4 - - - +
1025A GLN* 1.3 78.4 - - - +
1027A ALA* 1.3 62.1 + - - +
1083A ALA* 6.1 3.1 - - - +
1084A ASN 6.1 0.2 - - - +
1094A LEU* 3.5 41.1 - - + +
1095A ASN* 3.9 15.5 - - - +
1098A ALA* 3.4 2.6 - - - +
1141A TYR* 3.5 6.7 - - - -
1142A PHE* 2.8 36.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1027 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1026A ALA* 1.3 77.4 - - - +
1028A ALA* 1.3 60.8 + - - +
1042A HIS* 3.4 5.5 - - - +
1043A GLY* 3.3 25.2 + - - +
1080A VAL* 3.6 20.5 - - + +
1081A PRO* 5.0 8.1 - - + +
1083A ALA* 5.9 3.3 - - + +
1095A ASN* 3.6 2.5 + - - +
1098A ALA* 3.8 3.8 - - - -
1139A VAL* 5.3 4.3 - - + -
1140A GLY 3.3 12.1 - - - +
1141A TYR* 4.1 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1028 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1027A ALA* 1.3 76.1 - - - +
1029A LEU* 1.3 62.7 + - - +
1030A VAL* 5.1 3.8 - - + -
1041A THR 3.2 14.6 - - - +
1042A HIS* 3.9 2.9 - - + +
1080A VAL* 4.1 5.2 - - - -
1098A ALA* 3.9 16.4 - - + +
1099A VAL* 3.7 30.3 - - + +
1102A ALA* 5.2 0.4 - - - -
1139A VAL* 3.4 8.8 - - - +
1140A GLY 2.9 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1029 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1028A ALA* 1.3 75.0 - - - +
1030A VAL* 1.3 62.9 + - - +
1031A HIS* 3.7 34.6 - - + +
1039A LEU 3.9 1.4 - - - +
1040A VAL* 3.5 3.1 - - - -
1041A THR* 2.8 42.3 + - + +
1079A THR* 3.9 34.1 - - + +
1080A VAL* 4.2 5.4 - - + -
1137A SER* 4.2 7.0 - - - +
1138A ALA 3.6 8.5 - - - +
1139A VAL* 3.9 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1030 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1028A ALA* 5.1 2.5 - - + -
1029A LEU* 1.3 80.3 - - - +
1031A HIS* 1.3 65.8 + - - +
1032A ILE* 5.0 0.4 - - + -
1038A VAL* 3.8 25.4 - - + -
1039A LEU 3.6 3.1 - - - +
1040A VAL* 4.0 18.8 - - + -
1059A VAL* 5.5 1.3 - - + -
1063A LEU* 4.8 8.1 - - + -
1099A VAL* 4.6 7.2 - - + +
1102A ALA* 3.5 21.5 - - + -
1103A CYS* 4.8 8.7 - - - -
1106A LEU* 3.6 25.8 - - + +
1136A LEU 3.7 1.4 - - - +
1137A SER* 3.3 3.8 - - - -
1138A ALA 2.9 40.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1031 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1029A LEU* 3.7 35.1 - - + +
1030A VAL* 1.3 72.8 - - - +
1032A ILE* 1.3 65.4 + - - +
1033A TYR* 3.8 35.7 - + + -
1038A VAL* 3.4 9.9 - - - +
1039A LEU* 3.0 44.6 + - + +
1136A LEU 3.5 3.8 - - - +
1137A SER* 2.8 32.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1032 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1031A HIS* 1.3 77.1 - - - +
1033A TYR* 1.3 76.6 + - - +
1034A LEU* 4.7 1.4 - - - +
1036A GLY* 4.1 15.9 - - - +
1037A SER 3.7 3.1 - - - +
1038A VAL* 4.0 12.3 - - + -
1063A LEU* 4.6 7.4 - - + -
1106A LEU* 4.1 24.5 - - + -
1110A LEU* 4.2 11.4 - - + -
1122A TRP* 3.6 33.9 - - + -
1126A ALA* 4.0 17.7 - - + -
1136A LEU* 2.9 44.4 + - + +
----------------------------------------------------------
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