Contacts of the helix formed by residues 997 - 1014 (chain A) in PDB entry 4C48
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 SER 997 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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993A THR* 3.6 12.1 - - - +
994A GLY* 3.1 31.1 + - - -
996A GLY* 1.3 74.0 - - - +
998A GLY* 1.3 65.0 + - - +
999A ALA 3.1 3.8 + - - -
1000A GLN* 3.1 30.7 - - - +
1001A ASN* 3.3 30.2 + - - -
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Residues in contact with GLY 998 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565A PRO* 3.3 22.0 - - - +
567A GLU* 3.2 21.0 - - - +
996A GLY* 3.2 4.4 - - - -
997A SER* 1.3 78.3 + - - +
999A ALA* 1.3 60.7 + - - +
1001A ASN* 4.5 4.0 - - - +
1002A ALA* 3.5 13.7 + - - +
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Residues in contact with ALA 999 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396A PHE* 3.7 17.8 - - + -
565A PRO* 3.7 8.1 - - - -
567A GLU* 2.6 18.9 + - - +
926A TYR* 3.7 31.4 - - + +
996A GLY 5.1 0.9 - - - +
997A SER 3.1 1.0 + - - -
998A GLY* 1.3 72.4 - - - +
1000A GLN* 1.3 59.9 + - - +
1002A ALA* 2.8 25.6 + - - +
1003A VAL* 2.9 11.6 + - - +
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Residues in contact with GLN1000 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A GLU* 5.5 7.6 + - - +
340A VAL* 5.8 3.4 - - + -
343A THR* 5.8 3.6 - - + -
396A PHE* 3.3 24.9 - - + -
989A LEU* 3.1 47.5 - - + +
992A SER* 2.7 30.1 + - - -
994A GLY 4.4 2.6 + - - -
995A ALA 5.6 0.6 + - - -
996A GLY 3.5 7.2 + - - +
997A SER* 3.1 39.6 - - - +
999A ALA* 1.3 76.4 + - - +
1001A ASN* 1.3 54.7 + - - +
1004A GLY 3.0 22.0 + - - -
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Residues in contact with ASN1001 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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919A ARG* 3.0 37.3 - - - +
921A LEU* 4.3 4.0 - - + -
989A LEU 2.8 25.5 + - - +
990A VAL* 3.3 6.3 - - - +
992A SER* 2.8 21.2 + - - +
993A THR* 4.5 3.2 - - - +
997A SER* 3.3 33.2 + - - +
998A GLY* 4.5 3.9 - - - +
999A ALA 3.2 0.6 - - - -
1000A GLN* 1.3 77.1 - - - +
1002A ALA* 1.3 58.3 + - - +
1003A VAL 3.2 0.2 + - - -
1005A THR* 2.9 36.9 + - - +
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Residues in contact with ALA1002 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565A PRO* 4.7 2.7 - - + -
921A LEU* 3.5 24.0 - - + +
924A ASP* 4.1 20.7 - - - +
926A TYR* 4.3 16.3 - - + +
927A PHE* 4.5 10.4 + - - +
998A GLY 3.5 14.2 + - - +
999A ALA* 2.8 13.2 + - - +
1001A ASN* 1.3 75.4 - - - +
1003A VAL* 1.3 61.2 + - - +
1005A THR* 4.1 1.0 + - - -
1006A GLY* 3.8 12.5 + - - -
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Residues in contact with VAL1003 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396A PHE* 3.4 41.7 - - + -
399A VAL* 5.5 0.2 - - + -
400A LEU* 3.7 37.9 - - + +
926A TYR* 3.5 35.0 - - + +
929A VAL* 4.2 1.6 - - + -
930A GLY* 5.0 2.7 - - - +
989A LEU* 3.7 15.5 - - + -
999A ALA 2.9 6.2 + - - +
1000A GLN 4.2 0.2 - - - +
1002A ALA* 1.3 78.6 - - - +
1004A GLY* 1.3 60.9 + - - +
1006A GLY* 3.3 2.8 + - - -
1007A VAL* 3.0 26.7 + - - +
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Residues in contact with GLY1004 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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986A VAL* 4.8 2.5 - - - -
989A LEU* 4.4 7.2 - - - -
990A VAL* 3.2 20.3 - - - +
1000A GLN 3.0 15.3 + - - -
1003A VAL* 1.3 77.3 - - - +
1005A THR* 1.3 57.0 + - - +
1006A GLY 3.0 4.3 - - - -
1007A VAL* 3.2 13.0 + - - +
1008A MET* 2.8 31.7 + - - +
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Residues in contact with THR1005 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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915A ALA* 3.3 41.1 + - - +
916A ALA* 5.3 1.2 - - - +
919A ARG* 3.1 41.1 - - - +
921A LEU* 3.0 23.0 - - - +
990A VAL* 3.6 20.0 - - + -
1001A ASN 2.9 12.8 + - - +
1002A ALA 4.1 0.2 + - - -
1004A GLY* 1.3 74.9 - - - +
1006A GLY* 1.3 60.3 + - - +
1008A MET* 4.0 5.4 - - - -
1009A GLY 3.9 3.3 + - - -
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Residues in contact with GLY1006 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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912A ALA* 3.1 32.0 - - - +
916A ALA* 5.8 1.1 - - - -
927A PHE* 4.1 25.1 - - - -
930A GLY* 5.2 6.2 - - - -
934A THR* 4.2 1.6 - - - +
1002A ALA 3.8 8.3 + - - -
1003A VAL 3.3 8.9 + - - -
1004A GLY 3.0 0.8 - - - -
1005A THR* 1.3 81.5 + - - +
1007A VAL* 1.3 60.4 + - - +
1008A MET 3.3 0.2 - - - -
1010A GLY 3.8 0.3 + - - -
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Residues in contact with VAL1007 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A LEU* 4.4 11.7 - - + -
930A GLY* 5.0 3.7 - - - +
933A THR* 3.5 22.4 - - - +
934A THR* 3.6 16.6 - - + +
982A PHE* 3.4 28.0 - - + -
986A VAL* 3.9 27.1 - - + -
1003A VAL 3.0 14.2 + - - +
1004A GLY* 3.2 16.4 - - - +
1006A GLY* 1.3 75.0 - - - +
1008A MET* 1.3 61.9 + - - +
1011A MET* 2.9 29.9 + - + +
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Residues in contact with MET1008 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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915A ALA* 5.9 0.2 - - + -
983A ILE* 3.6 22.6 - - + +
986A VAL* 3.4 29.8 - - + -
987A MET* 3.4 32.1 - - + -
990A VAL* 3.7 23.3 - - + -
1004A GLY 2.8 15.3 + - - +
1005A THR* 4.4 4.9 - - - -
1006A GLY 3.3 0.2 - - - -
1007A VAL* 1.3 76.5 - - - +
1009A GLY* 1.3 62.5 + - - +
1011A MET* 2.7 26.0 + - - +
1012A VAL* 2.9 16.7 + - + +
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Residues in contact with GLY1009 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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911A GLY* 3.3 28.7 - - - -
914A LEU* 5.4 1.8 - - - -
915A ALA* 3.8 11.7 - - - +
1005A THR 3.9 7.7 + - - -
1008A MET* 1.3 79.3 - - - +
1010A GLY* 1.3 61.5 + - - +
1012A VAL* 3.0 29.8 - - - +
1013A THR 3.1 5.7 + - - -
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Residues in contact with GLY1010 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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908A GLY* 3.0 25.5 - - - +
912A ALA* 2.9 23.5 - - - +
934A THR* 4.3 11.5 - - - -
1006A GLY 3.8 2.8 + - - -
1007A VAL 3.7 3.8 - - - -
1008A MET 3.1 0.8 - - - -
1009A GLY* 1.3 74.1 - - - +
1011A MET* 1.3 57.1 + - - +
1014A ALA* 2.9 29.2 + - - +
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Residues in contact with MET1011 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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934A THR* 5.1 3.1 - - + +
937A LEU* 3.7 30.1 - - + -
938A SER* 6.3 0.2 - - - -
941A ASN* 5.4 3.8 - - - +
978A THR* 5.3 1.6 - - - +
979A SER* 3.6 41.7 - - - +
982A PHE* 3.3 39.9 - - + -
983A ILE* 5.1 11.2 - - + -
1007A VAL* 2.9 22.0 + - + +
1008A MET* 2.7 16.6 + - - +
1010A GLY* 1.3 72.6 - - - +
1012A VAL* 1.3 53.9 + - - +
1014A ALA* 3.5 5.9 + - - -
1015A THR* 2.5 44.9 + - + +
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Residues in contact with VAL1012 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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914A LEU* 6.4 0.4 - - + -
983A ILE* 3.8 27.6 - - + -
1008A MET* 2.9 13.6 + - + +
1009A GLY* 3.0 23.3 - - - +
1011A MET* 1.3 75.1 - - - +
1013A THR* 1.3 77.3 + - + +
1015A THR* 2.6 30.5 + - - -
1016A VAL* 2.9 23.4 + - + +
22C ILE* 4.8 11.4 - - + -
25C LEU* 5.2 8.5 - - + -
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Residues in contact with THR1013 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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907A LEU* 2.7 28.6 + - - +
908A GLY 2.8 18.9 + - - -
910A ILE* 4.6 8.5 - - + -
911A GLY* 3.1 28.8 + - - +
914A LEU* 5.2 4.5 - - + -
1009A GLY 3.1 4.1 + - - +
1012A VAL* 1.3 82.6 - - + +
1014A ALA* 1.3 57.2 + - - +
1015A THR 3.2 0.7 - - - -
1016A VAL* 4.2 9.2 - - + -
1017A LEU* 3.0 36.1 - - + +
1018A ALA 3.7 2.3 + - - -
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Residues in contact with ALA1014 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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908A GLY* 3.6 13.5 - - - +
934A THR 4.8 3.6 - - - +
938A SER* 3.5 31.2 - - - -
941A ASN* 4.4 7.7 + - - +
1010A GLY 2.9 20.7 + - - +
1011A MET* 4.0 10.8 - - - +
1012A VAL 2.9 1.0 + - - -
1013A THR* 1.3 79.5 + - - +
1015A THR* 1.3 61.6 + - + +
1018A ALA* 3.0 24.4 - - - +
1019A ILE* 5.6 0.3 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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