Contacts of the helix formed by residues 981 - 1003 (chain H) in PDB entry 6X34
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 GLN 981 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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980H ALA* 1.3 78.8 - - - +
982H THR* 1.3 57.3 + - - +
984H LEU* 3.3 6.5 + - - +
985H VAL* 2.9 30.1 + - - +
1040H CYS* 6.0 0.9 - - - -
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Residues in contact with THR 982 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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980H ALA 3.3 3.6 - - - +
981H GLN* 1.3 77.2 - - - +
983H THR* 1.3 58.6 + - - +
985H VAL* 3.3 6.8 + - - +
986H ASP* 2.9 29.5 + - - +
1036H ARG* 5.6 2.7 - - - +
1040H CYS* 5.3 6.5 - - - -
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Residues in contact with THR 983 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
980H ALA* 3.4 17.6 + - - +
981H GLN 3.3 0.4 - - - -
982H THR* 1.3 77.8 - - - +
984H LEU* 1.3 57.3 + - - +
986H ASP* 3.3 6.8 + - - +
987H ARG* 2.9 29.9 + - - +
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Residues in contact with LEU 984 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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935H LEU* 5.2 14.4 - - + -
980H ALA 2.9 17.4 + - - +
981H GLN* 3.7 7.6 - - - +
983H THR* 1.3 77.6 - - - +
985H VAL* 1.3 55.7 + - - +
987H ARG* 3.3 6.5 + - - +
988H LEU* 2.9 29.1 + - - +
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Residues in contact with VAL 985 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
981H GLN 2.9 17.6 + - - +
982H THR 3.7 4.3 - - - +
983H THR 3.3 0.2 - - - -
984H LEU* 1.3 75.4 - - - +
986H ASP* 1.3 58.7 + - - +
988H LEU* 3.3 6.4 + - - +
989H ALA* 2.9 30.2 + - - +
1035H ASN 4.6 3.0 - - - +
1036H ARG* 4.8 3.1 - - - +
1039H LEU* 4.7 5.9 - - + +
1040H CYS* 3.7 39.5 - - + +
1043H VAL* 5.4 6.3 - - + -
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Residues in contact with ASP 986 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
982H THR 2.9 17.6 + - - +
983H THR* 3.7 7.4 - - - +
985H VAL* 1.3 77.9 - - - +
987H ARG* 1.3 56.3 + - - +
989H ALA* 3.3 6.9 + - - +
990H GLU* 2.9 29.6 + - - +
1036H ARG* 5.0 16.7 - - + +
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Residues in contact with ARG 987 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
983H THR 2.9 17.6 + - - +
984H LEU* 3.7 7.9 - - - +
986H ASP* 1.3 76.7 - - - +
988H LEU* 1.3 57.3 + - - +
990H GLU* 3.3 6.6 + - - +
991H ASN* 2.9 29.1 + - - +
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Residues in contact with LEU 988 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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931H THR* 3.7 36.2 - - - +
984H LEU 2.9 17.6 + - - +
985H VAL* 3.7 7.4 - - - +
987H ARG* 1.3 78.1 - - - +
989H ALA* 1.3 56.8 + - - +
991H ASN* 3.3 6.9 + - - +
992H GLY* 2.9 25.5 + - - -
1039H LEU* 6.3 1.6 - - + -
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Residues in contact with ALA 989 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
985H VAL 2.9 14.1 + - - +
986H ASP* 3.7 5.8 - - - +
987H ARG 3.3 0.2 - - - -
988H LEU* 1.3 76.5 - - - +
990H GLU* 1.3 56.1 + - - +
992H GLY* 3.3 1.6 + - - -
993H HIS* 2.5 41.9 + - + -
1035H ASN* 3.5 43.3 - - + +
1039H LEU* 4.7 6.8 - - + +
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Residues in contact with GLU 990 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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986H ASP 2.9 17.2 + - - +
987H ARG* 3.7 7.6 - - - +
989H ALA* 1.3 77.7 - - - +
991H ASN* 1.3 55.7 + - - +
993H HIS* 3.3 7.5 + - - +
994H ASN* 2.9 30.0 + - - +
1024H TYR* 4.2 26.2 + - + +
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Residues in contact with ASN 991 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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854H CYS 5.0 3.1 - - - +
855H PRO* 4.6 17.7 - - - +
987H ARG 2.9 17.1 + - - +
988H LEU* 3.7 7.0 - - - +
990H GLU* 1.3 75.8 - - - +
992H GLY* 1.3 58.1 + - - +
994H ASN* 3.3 7.0 + - - +
995H VAL* 2.9 28.9 + - - +
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Residues in contact with GLY 992 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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988H LEU 2.9 15.3 + - - -
989H ALA* 3.7 3.6 - - - -
991H ASN* 1.3 77.0 - - - +
993H HIS* 1.3 57.6 + - - +
995H VAL* 3.3 6.5 + - - +
996H TRP* 2.9 28.8 + - - +
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Residues in contact with HIS 993 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
989H ALA* 2.5 37.0 + - + +
990H GLU* 3.7 6.5 - - - +
992H GLY* 1.3 76.0 - - - +
994H ASN* 1.3 58.0 + - - +
996H TRP* 3.3 15.2 + + + +
997H ALA* 2.9 29.5 + - - +
1022H VAL 5.7 2.7 - - - +
1023H PRO* 5.8 1.3 - - - -
1024H TYR* 5.5 7.0 - - - +
1031H THR* 4.9 10.6 + - - -
1032H LYS* 6.1 0.2 - - - -
1035H ASN* 3.5 32.0 - - + +
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Residues in contact with ASN 994 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
853H PRO* 3.8 8.6 - - + +
854H CYS 3.3 33.2 - - - +
855H PRO* 5.1 0.9 - - - -
990H GLU 2.9 17.6 + - - +
991H ASN* 3.7 3.8 - - - +
993H HIS* 1.3 77.5 - - - +
995H VAL* 1.3 57.5 + - - +
997H ALA* 3.3 6.5 + - - +
998H ARG* 2.9 29.1 + - - +
1023H PRO* 4.8 13.5 - - + -
1024H TYR* 5.2 4.4 - - + +
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Residues in contact with VAL 995 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855H PRO* 3.9 23.5 - - + +
991H ASN 2.9 18.0 + - - +
992H GLY* 3.3 7.8 + - - +
994H ASN* 1.3 76.3 - - - +
996H TRP* 1.3 57.0 + - - +
998H ARG* 3.3 4.4 + - - +
999H ASP* 2.9 29.9 + - - +
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Residues in contact with TRP 996 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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992H GLY 2.9 17.1 + - - +
993H HIS* 3.6 13.9 - + + +
995H VAL* 1.3 77.0 - - - +
997H ALA* 1.3 73.2 + - + +
999H ASP* 3.3 7.6 + - + +
1000H ARG* 2.9 41.1 + - + +
1018H ASN* 4.6 18.4 - - + -
1020H ARG 4.3 10.5 - - - -
1021H LEU* 4.2 21.5 - - + -
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Residues in contact with ALA 997 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657H THR* 5.5 6.5 - - + +
853H PRO* 4.8 8.7 - - + -
993H HIS 2.9 17.3 + - - +
994H ASN* 3.7 7.6 - - - +
996H TRP* 1.3 88.4 - - + +
998H ARG* 1.3 58.0 + - - +
1000H ARG* 3.3 5.2 + - - +
1001H VAL* 2.9 29.9 + - - +
1021H LEU* 3.8 26.2 - - + +
1022H VAL 5.3 0.9 - - - +
1023H PRO* 5.2 4.5 - - + -
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Residues in contact with ARG 998 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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853H PRO* 4.5 15.8 - - + +
855H PRO* 5.7 5.8 - - + -
994H ASN 2.9 17.8 + - - +
995H VAL* 3.7 7.4 - - - +
997H ALA* 1.3 76.4 - - - +
999H ASP* 1.3 57.0 + - - +
1001H VAL* 3.3 7.2 + - - +
1002H ALA* 2.9 29.1 + - - +
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Residues in contact with ASP 999 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
995H VAL 2.9 17.5 + - - +
996H TRP* 3.3 9.4 + - + +
998H ARG* 1.3 75.5 - - - +
1000H ARG* 1.3 57.8 + - - +
1002H ALA* 3.3 7.4 + - - +
1003H GLN* 2.9 28.8 + - - +
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Residues in contact with ARG1000 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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996H TRP* 2.9 34.2 + - + +
997H ALA* 3.7 7.9 - - - +
999H ASP* 1.3 75.7 - - - +
1001H VAL* 1.3 61.3 + - - +
1003H GLN* 3.2 15.7 + - - +
1004H GLY 3.4 1.2 + - - -
1005H TRP* 3.1 27.6 + - + +
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Residues in contact with VAL1001 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655H GLY* 5.2 11.7 - - - +
656H THR 5.0 11.4 - - - +
657H THR* 5.5 7.4 - - + -
997H ALA 2.9 17.4 + - - +
998H ARG* 3.7 7.2 - - - +
999H ASP 3.3 0.2 - - - -
1000H ARG* 1.3 76.3 - - - +
1002H ALA* 1.3 63.3 + - - +
1004H GLY* 3.1 11.3 + - - -
1005H TRP* 3.7 17.7 + - + +
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Residues in contact with ALA1002 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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998H ARG 2.9 16.9 + - - +
999H ASP* 3.7 7.9 - - - +
1000H ARG 3.3 0.4 - - - -
1001H VAL* 1.3 76.3 - - - +
1003H GLN* 1.3 57.9 + - - +
1004H GLY* 3.1 3.7 + - - -
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Residues in contact with GLN1003 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
999H ASP 2.9 17.3 + - - +
1000H ARG* 3.6 9.9 - - - +
1001H VAL 3.2 0.6 - - - -
1002H ALA* 1.3 75.7 - - - +
1004H GLY* 1.3 59.7 + - - +
1016H ARG* 5.8 0.2 - - - +
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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
------------------------------------------------------------
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) + - + + + + + -
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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