Contacts of the helix formed by residues 981 - 1003 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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980D ALA* 1.3 79.0 - - - +
982D THR* 1.3 58.8 + - - +
984D LEU* 3.3 6.7 + - - +
985D VAL* 2.9 29.8 + - - +
1040D CYS* 6.0 0.9 - - - -
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Residues in contact with THR 982 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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980D ALA 3.3 3.9 - - - +
981D GLN* 1.3 78.2 - - - +
983D THR* 1.3 57.4 + - - +
985D VAL* 3.3 6.5 + - - +
986D ASP* 2.9 29.1 + - - +
1036D ARG* 5.6 2.3 - - - +
1040D CYS* 5.3 6.7 - - - -
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Residues in contact with THR 983 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
980D ALA* 3.4 17.6 + - - +
981D GLN 3.3 0.4 - - - -
982D THR* 1.3 78.1 - - - +
984D LEU* 1.3 58.0 + - - +
986D ASP* 3.3 6.4 + - - +
987D ARG* 2.9 29.1 + - - +
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Residues in contact with LEU 984 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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935D LEU* 5.2 14.4 - - + -
980D ALA 2.9 18.3 + - - +
981D GLN* 3.7 6.7 - - - +
983D THR* 1.3 76.4 - - - +
985D VAL* 1.3 58.1 + - - +
987D ARG* 3.3 7.1 + - - +
988D LEU* 2.9 29.1 + - - +
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Residues in contact with VAL 985 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
981D GLN 2.9 17.2 + - - +
982D THR 3.7 3.8 - - - +
984D LEU* 1.3 75.7 - - - +
986D ASP* 1.3 59.2 + - - +
988D LEU* 3.3 6.8 + - - +
989D ALA* 2.9 29.1 + - - +
1035D ASN 4.6 3.2 - - - +
1036D ARG* 4.8 2.9 - - - +
1039D LEU* 4.7 6.6 - - + +
1040D CYS* 3.7 39.3 - - + +
1043D VAL* 5.4 5.8 - - + -
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Residues in contact with ASP 986 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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982D THR 2.9 17.4 + - - +
983D THR* 3.7 7.9 - - - +
985D VAL* 1.3 76.8 - - - +
987D ARG* 1.3 55.6 + - - +
989D ALA* 3.3 6.9 + - - +
990D GLU* 2.9 29.5 + - - +
1036D ARG* 5.0 16.7 - - + +
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Residues in contact with ARG 987 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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983D THR 2.9 17.1 + - - +
984D LEU* 3.7 7.4 - - - +
986D ASP* 1.3 75.7 - - - +
988D LEU* 1.3 58.1 + - - +
990D GLU* 3.7 6.5 - - - +
991D ASN* 2.9 29.5 + - - +
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Residues in contact with LEU 988 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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931D THR* 3.7 35.7 - - - +
984D LEU 2.9 17.6 + - - +
985D VAL* 3.7 8.3 - - - +
987D ARG* 1.3 77.9 - - - +
989D ALA* 1.3 56.1 + - - +
991D ASN* 3.3 6.7 + - - +
992D GLY* 2.9 25.6 + - - -
1039D LEU* 6.3 1.1 - - + -
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Residues in contact with ALA 989 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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985D VAL 2.9 14.9 + - - +
986D ASP* 3.7 5.8 - - - +
988D LEU* 1.3 75.6 - - - +
990D GLU* 1.3 56.6 + - - +
992D GLY* 3.3 1.9 + - - +
993D HIS* 2.5 41.5 + - + -
1035D ASN* 3.5 42.4 - - + +
1039D LEU* 4.7 7.1 - - + +
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Residues in contact with GLU 990 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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986D ASP 2.9 17.6 + - - +
987D ARG* 3.7 7.0 - - - +
989D ALA* 1.3 77.5 - - - +
991D ASN* 1.3 57.1 + - - +
993D HIS* 3.3 7.2 + - - +
994D ASN* 2.9 30.3 + - - +
1024D TYR* 4.2 27.3 - - + +
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Residues in contact with ASN 991 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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854D CYS 5.0 3.6 - - - +
855D PRO* 4.6 17.9 - - - +
987D ARG 2.9 18.2 + - - +
988D LEU* 3.7 7.4 - - - +
990D GLU* 1.3 75.3 - - - +
992D GLY* 1.3 58.7 + - - +
994D ASN* 3.3 6.2 + - - +
995D VAL* 2.9 29.2 + - - +
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Residues in contact with GLY 992 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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988D LEU 2.9 15.6 + - - -
989D ALA* 3.7 2.9 - - - -
991D ASN* 1.3 77.1 - - - +
993D HIS* 1.3 57.5 + - - +
995D VAL* 3.3 6.6 + - - +
996D TRP* 2.9 29.3 + - - +
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Residues in contact with HIS 993 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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989D ALA* 2.5 37.2 + - + +
990D GLU* 3.7 6.7 - - - +
992D GLY* 1.3 76.5 - - - +
994D ASN* 1.3 57.6 + - - +
996D TRP* 3.3 14.8 + + + +
997D ALA* 2.9 29.3 + - - +
1022D VAL 5.7 2.5 - - - +
1023D PRO* 5.8 1.8 - - - -
1024D TYR* 5.5 7.2 - - - +
1031D THR* 4.9 11.0 + - - -
1032D LYS* 6.1 0.2 - - - -
1035D ASN* 3.5 31.3 - - + +
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Residues in contact with ASN 994 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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853D PRO* 3.8 9.1 - - + +
854D CYS 3.3 34.3 - - - +
855D PRO* 5.1 0.9 - - - -
990D GLU 2.9 17.6 + - - +
991D ASN* 3.7 3.4 - - - +
993D HIS* 1.3 78.5 - - - +
995D VAL* 1.3 57.6 + - - +
997D ALA* 3.3 7.2 + - - +
998D ARG* 2.9 29.5 + - - +
1023D PRO* 4.8 12.6 - - + -
1024D TYR* 5.2 4.9 - - + +
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Residues in contact with VAL 995 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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855D PRO* 3.9 22.8 - - + +
991D ASN 2.9 17.2 + - - +
992D GLY* 3.3 7.6 + - - +
994D ASN* 1.3 76.7 - - - +
996D TRP* 1.3 58.0 + - - +
998D ARG* 3.3 4.9 + - - +
999D ASP* 2.9 29.5 + - - +
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Residues in contact with TRP 996 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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992D GLY 2.9 17.6 + - - +
993D HIS* 3.6 13.9 - + + +
995D VAL* 1.3 77.9 - - - +
997D ALA* 1.3 72.7 + - + +
999D ASP* 3.3 8.3 + - + +
1000D ARG* 2.9 40.5 + - + +
1018D ASN* 4.6 18.2 - - + -
1020D ARG 4.3 10.5 - - - -
1021D LEU* 4.2 21.1 - - + -
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Residues in contact with ALA 997 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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657D THR* 5.5 6.9 - - + +
853D PRO* 4.8 8.3 - - + -
993D HIS 2.9 17.2 + - - +
994D ASN* 3.7 7.4 - - - +
996D TRP* 1.3 88.1 - - + +
998D ARG* 1.3 58.1 + - - +
1000D ARG* 3.3 5.6 + - - +
1001D VAL* 2.9 29.3 + - - +
1021D LEU* 3.8 26.5 - - + +
1022D VAL 5.3 0.7 - - - +
1023D PRO* 5.2 5.4 - - + -
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Residues in contact with ARG 998 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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853D PRO* 4.5 15.9 - - + +
855D PRO* 5.7 5.6 - - + -
994D ASN 2.9 16.8 + - - +
995D VAL* 3.7 8.1 - - - +
997D ALA* 1.3 77.9 - - - +
999D ASP* 1.3 56.1 + - - +
1001D VAL* 3.3 7.1 + - - +
1002D ALA* 2.9 29.5 + - - +
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Residues in contact with ASP 999 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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995D VAL 2.9 17.6 + - - +
996D TRP* 3.7 9.9 - - + +
998D ARG* 1.3 75.7 - - - +
1000D ARG* 1.3 58.6 + - - +
1002D ALA* 3.3 7.7 + - - +
1003D GLN* 2.9 28.8 + - - +
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Residues in contact with ARG1000 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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996D TRP* 2.9 35.1 + - + +
997D ALA* 3.7 7.4 - - - +
999D ASP* 1.3 77.1 - - - +
1001D VAL* 1.3 62.4 + - - +
1003D GLN* 3.2 15.5 + - - +
1004D GLY 3.4 1.2 + - - -
1005D TRP* 3.1 27.3 + - + +
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Residues in contact with VAL1001 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655D GLY* 5.2 11.4 - - - +
656D THR 5.0 11.2 - - - +
657D THR* 5.5 8.1 - - + -
997D ALA 2.9 17.8 + - - +
998D ARG* 3.7 7.4 - - - +
999D ASP 3.3 0.2 - - - -
1000D ARG* 1.3 76.3 - - - +
1002D ALA* 1.3 62.1 + - - +
1004D GLY* 3.1 11.1 + - - -
1005D TRP* 3.7 17.3 + - + +
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Residues in contact with ALA1002 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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998D ARG 2.9 17.2 + - - +
999D ASP* 3.7 7.4 - - - +
1000D ARG 3.3 0.2 - - - -
1001D VAL* 1.3 77.1 - - - +
1003D GLN* 1.3 57.4 + - - +
1004D GLY 3.1 4.1 + - - -
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Residues in contact with GLN1003 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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999D ASP 2.9 17.3 + - - +
1000D ARG* 3.6 10.8 - - - +
1001D VAL 3.2 1.0 - - - -
1002D ALA* 1.3 73.6 - - - +
1004D GLY* 1.3 59.8 + - - +
1016D ARG* 5.8 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