Contacts of the helix formed by residues 981 - 1003 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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980F ALA* 1.3 80.7 - - - +
982F THR* 1.3 57.8 + - - +
984F LEU* 3.3 6.2 + - - +
985F VAL* 2.9 30.0 + - - +
1040F CYS* 6.0 0.9 - - - -
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Residues in contact with THR 982 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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980F ALA 3.3 4.1 - - - +
981F GLN* 1.3 76.1 - - - +
983F THR* 1.3 58.0 + - - +
985F VAL* 3.3 6.6 + - - +
986F ASP* 2.9 29.5 + - - +
1036F ARG* 5.6 2.0 - - - +
1040F CYS* 5.3 6.5 - - - -
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Residues in contact with THR 983 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
980F ALA* 3.4 18.7 + - - +
981F GLN 3.3 0.8 - - - -
982F THR* 1.3 78.5 - - - +
984F LEU* 1.3 58.0 + - - +
986F ASP* 3.3 7.3 + - - +
987F ARG* 2.9 29.1 + - - +
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Residues in contact with LEU 984 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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935F LEU* 5.2 14.4 - - + -
980F ALA 2.9 18.0 + - - +
981F GLN* 3.7 7.4 - - - +
983F THR* 1.3 76.3 - - - +
985F VAL* 1.3 58.2 + - - +
987F ARG* 3.3 7.0 + - - +
988F LEU* 2.9 28.8 + - - +
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Residues in contact with VAL 985 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
981F GLN 2.9 17.6 + - - +
982F THR 3.7 4.0 - - - +
984F LEU* 1.3 76.5 - - - +
986F ASP* 1.3 58.2 + - - +
988F LEU* 3.3 7.0 + - - +
989F ALA* 2.9 29.8 + - - +
1035F ASN 4.6 3.2 - - - +
1036F ARG* 4.8 2.9 - - - +
1039F LEU* 4.7 5.5 - - + +
1040F CYS* 3.7 39.7 - - + +
1043F VAL* 5.4 5.8 - - + -
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Residues in contact with ASP 986 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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982F THR 2.9 17.8 + - - +
983F THR* 3.7 7.0 - - - +
984F LEU 3.3 0.2 - - - -
985F VAL* 1.3 77.7 - - - +
987F ARG* 1.3 56.2 + - - +
989F ALA* 3.3 7.0 + - - +
990F GLU* 2.9 29.5 + - - +
1036F ARG* 5.0 17.4 - - + +
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Residues in contact with ARG 987 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
983F THR 2.9 17.2 + - - +
984F LEU* 3.7 7.2 - - - +
986F ASP* 1.3 75.8 - - - +
988F LEU* 1.3 57.6 + - - +
990F GLU* 3.3 7.8 + - - +
991F ASN* 2.9 29.5 + - - +
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Residues in contact with LEU 988 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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931F THR* 3.7 36.4 - - - +
984F LEU 2.9 17.2 + - - +
985F VAL* 3.7 7.2 - - - +
987F ARG* 1.3 77.5 - - - +
989F ALA* 1.3 56.6 + - - +
991F ASN* 3.3 6.9 + - - +
992F GLY* 2.9 24.8 + - - -
1039F LEU* 6.3 1.1 - - + -
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Residues in contact with ALA 989 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
985F VAL 2.9 14.2 + - - +
986F ASP* 3.7 6.5 - - - +
988F LEU* 1.3 76.0 - - - +
990F GLU* 1.3 56.9 + - - +
992F GLY* 3.3 1.9 + - - +
993F HIS* 2.5 41.7 + - + -
1035F ASN* 3.5 41.7 - - + +
1036F ARG* 5.4 0.2 - - - -
1039F LEU* 4.7 7.4 - - + +
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Residues in contact with GLU 990 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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986F ASP 2.9 17.8 + - - +
987F ARG* 3.7 7.4 - - - +
988F LEU 3.3 0.2 - - - -
989F ALA* 1.3 76.6 - - - +
991F ASN* 1.3 57.3 + - - +
993F HIS* 3.3 6.9 + - - +
994F ASN* 2.9 29.7 + - - +
1024F TYR* 4.2 26.7 - - + +
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Residues in contact with ASN 991 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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854F CYS 5.0 3.1 - - - +
855F PRO* 4.6 17.0 - - - +
987F ARG 2.9 17.6 + - - +
988F LEU* 3.7 7.2 - - - +
990F GLU* 1.3 76.2 - - - +
992F GLY* 1.3 58.2 + - - +
994F ASN* 3.3 7.0 + - - +
995F VAL* 2.9 29.7 + - - +
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Residues in contact with GLY 992 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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988F LEU 2.9 15.7 + - - -
989F ALA* 3.7 3.1 - - - -
991F ASN* 1.3 77.5 - - - +
993F HIS* 1.3 57.8 + - - +
995F VAL* 3.3 6.9 + - - +
996F TRP* 2.9 28.8 + - - +
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Residues in contact with HIS 993 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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989F ALA* 2.5 37.7 + - + +
990F GLU* 3.7 7.0 - - - +
991F ASN 3.3 0.2 - - - -
992F GLY* 1.3 75.8 - - - +
994F ASN* 1.3 57.1 + - - +
996F TRP* 3.3 14.9 + + + +
997F ALA* 2.9 28.4 + - - +
1022F VAL 5.7 2.9 - - - +
1023F PRO* 5.8 1.3 - - - -
1024F TYR* 5.5 7.2 - - - +
1031F THR* 4.9 11.0 + - - -
1032F LYS* 6.1 0.2 - - - -
1035F ASN* 3.5 31.6 - - + +
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Residues in contact with ASN 994 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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853F PRO* 3.8 9.0 - - + +
854F CYS 3.3 33.4 - - - +
855F PRO* 5.1 0.9 - - - -
990F GLU 2.9 17.9 + - - +
991F ASN* 3.7 3.8 - - - +
992F GLY 3.3 0.2 - - - -
993F HIS* 1.3 77.0 - - - +
995F VAL* 1.3 56.1 + - - +
997F ALA* 3.3 7.0 + - - +
998F ARG* 2.9 29.9 + - - +
1023F PRO* 4.8 14.4 - - + -
1024F TYR* 5.2 4.4 - - + +
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Residues in contact with VAL 995 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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855F PRO* 3.9 23.0 - - + +
991F ASN 2.9 17.2 + - - +
992F GLY* 3.7 7.2 - - - +
994F ASN* 1.3 75.7 - - - +
996F TRP* 1.3 57.7 + - - +
998F ARG* 3.3 4.0 + - - +
999F ASP* 2.9 29.8 + - - +
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Residues in contact with TRP 996 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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992F GLY 2.9 17.1 + - - +
993F HIS* 3.6 14.6 - + + +
995F VAL* 1.3 77.4 - - - +
997F ALA* 1.3 72.3 + - + +
999F ASP* 3.3 8.5 + - + +
1000F ARG* 2.9 39.1 + - + +
1018F ASN* 4.6 18.4 - - + -
1020F ARG 4.3 11.0 - - - -
1021F LEU* 4.2 21.5 - - + -
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Residues in contact with ALA 997 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657F THR* 5.5 7.0 - - + +
853F PRO* 4.8 8.1 - - + -
993F HIS 2.9 16.5 + - - +
994F ASN* 3.7 7.9 - - - +
995F VAL 3.3 0.2 - - - -
996F TRP* 1.3 88.5 - - + +
998F ARG* 1.3 57.1 + - - +
1000F ARG* 3.3 5.4 + - - +
1001F VAL* 2.9 29.7 + - - +
1021F LEU* 3.8 25.8 - - + +
1022F VAL 5.3 0.7 - - - +
1023F PRO* 5.2 5.6 - - + -
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Residues in contact with ARG 998 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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853F PRO* 4.5 15.9 - - + +
855F PRO* 5.7 5.8 - - + -
994F ASN 2.9 18.0 + - - +
995F VAL* 3.7 7.2 - - - +
997F ALA* 1.3 77.3 - - - +
999F ASP* 1.3 56.4 + - - +
1001F VAL* 3.3 6.0 + - - +
1002F ALA* 2.9 29.7 + - - +
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Residues in contact with ASP 999 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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995F VAL 2.9 16.9 + - - +
996F TRP* 3.3 9.4 + - + +
998F ARG* 1.3 75.6 - - - +
1000F ARG* 1.3 57.1 + - - +
1002F ALA* 3.3 7.1 + - - +
1003F GLN* 2.9 28.1 + - - +
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Residues in contact with ARG1000 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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996F TRP* 2.9 35.1 + - + +
997F ALA* 3.7 7.4 - - - +
998F ARG 3.3 0.4 - - - -
999F ASP* 1.3 75.5 - - - +
1001F VAL* 1.3 62.0 + - - +
1003F GLN* 3.2 15.6 + - - +
1004F GLY 3.4 1.6 + - - -
1005F TRP* 3.1 27.4 + - + +
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Residues in contact with VAL1001 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655F GLY* 5.2 11.7 - - - +
656F THR 5.0 11.4 - - - +
657F THR* 5.5 7.9 - - + -
997F ALA 2.9 17.4 + - - +
998F ARG* 3.7 7.6 - - - +
1000F ARG* 1.3 75.7 - - - +
1002F ALA* 1.3 61.9 + - - +
1004F GLY* 3.1 11.8 + - - -
1005F TRP* 3.7 17.5 + - + +
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Residues in contact with ALA1002 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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998F ARG 2.9 17.0 + - - +
999F ASP* 3.7 7.9 - - - +
1001F VAL* 1.3 76.4 - - - +
1003F GLN* 1.3 56.3 + - - +
1004F GLY 3.1 3.7 + - - -
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Residues in contact with GLN1003 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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999F ASP 2.9 17.5 + - - +
1000F ARG* 3.6 9.9 - - - +
1001F VAL 3.2 0.8 - - - -
1002F ALA* 1.3 73.8 - - - +
1004F GLY* 1.3 60.6 + - - +
1016F 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