Contacts of the helix formed by residues 941 - 953 (chain D) in PDB entry 3BBT
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 LYS 941 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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810D GLU* 4.4 15.9 - - - +
875D GLN* 3.7 25.1 - - - +
878D VAL* 4.7 0.4 - - - -
937D ASP 6.1 0.2 - - - +
939D ARG 3.8 2.4 + - - +
940D PRO* 1.3 75.5 - - - +
942D PHE* 1.3 60.3 + - - +
943D LYS* 3.1 35.0 - - + +
944D GLU* 2.9 37.6 + - - +
945D LEU* 3.1 12.3 + - - +
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Residues in contact with PHE 942 (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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803D ALA* 3.9 14.1 - - - +
806D MET* 3.6 52.0 - - + -
807D MET* 3.8 20.2 - - + +
810D GLU* 3.8 24.1 + - + +
874D HIS* 3.5 24.0 - - + -
875D GLN* 6.0 0.4 - - - -
877D ASP* 3.6 28.5 - - + -
878D VAL* 3.7 7.4 - - + +
881D TYR* 3.6 26.0 - + + -
940D PRO 4.3 0.2 + - - -
941D LYS* 1.3 71.8 - - - +
943D LYS* 1.3 56.6 + - - +
945D LEU* 3.7 18.8 - - + +
946D ALA* 2.9 29.8 + - - +
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Residues in contact with LYS 943 (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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954B ARG* 5.3 17.8 + - - +
807D MET* 3.7 27.9 - - + +
810D GLU* 5.4 7.2 + - - -
811D GLU* 5.9 1.4 + - - -
941D LYS* 3.0 37.3 + - + +
942D PHE* 1.3 78.8 - - - +
944D GLU* 1.3 66.2 + - + +
946D ALA* 3.4 2.8 + - - +
947D ALA* 2.9 30.9 + - - +
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Residues in contact with GLU 944 (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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940D PRO* 3.3 18.3 - - + +
941D LYS* 2.9 37.3 + - - +
943D LYS* 1.3 82.4 - - + +
945D LEU* 1.3 59.6 + - - +
947D ALA* 3.8 5.6 - - - +
948D GLU* 2.9 33.3 + - - +
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Residues in contact with LEU 945 (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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803D ALA* 4.4 5.2 - - + -
878D VAL* 4.3 17.7 - - + -
881D TYR* 3.7 30.5 - - + -
927D VAL* 3.6 30.3 - - + -
931D CYS* 3.8 16.4 - - - -
940D PRO* 4.1 12.3 - - + +
941D LYS 3.1 11.8 + - - +
942D PHE* 3.7 38.8 - - + +
944D GLU* 1.3 73.9 - - - +
946D ALA* 1.3 64.9 + - - +
948D GLU* 3.9 2.9 - - - -
949D PHE* 3.0 34.2 + - + +
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Residues in contact with ALA 946 (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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800D VAL* 4.2 10.7 - - + +
803D ALA* 3.8 17.4 - - + +
804D LYS* 4.4 15.9 - - + -
807D MET* 3.8 18.4 - - - -
942D PHE 2.9 19.6 + - - +
943D LYS 3.6 4.5 - - - +
945D LEU* 1.3 76.7 - - - +
947D ALA* 1.3 57.1 + - - +
949D PHE 3.9 0.2 - - - -
950D SER* 2.9 32.5 + - - -
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Residues in contact with ALA 947 (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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954B ARG* 5.6 7.2 - - - +
943D LYS 2.9 18.8 + - - +
944D GLU* 3.9 6.7 - - - +
946D ALA* 1.3 76.5 - - - +
948D GLU* 1.3 61.4 + - - +
950D SER* 3.9 5.9 - - - -
951D ARG* 3.4 22.5 + - - +
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Residues in contact with GLU 948 (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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927D VAL* 4.3 25.5 - - + +
944D GLU 2.9 19.1 + - - +
945D LEU* 4.0 4.5 - - - +
947D ALA* 1.3 75.4 - - - +
949D PHE* 1.3 64.8 + - + +
951D ARG* 2.8 64.7 + - - +
952D MET* 3.4 24.2 - - + +
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Residues in contact with PHE 949 (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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796D LEU* 4.1 17.3 - - + +
799D CYS* 3.8 23.3 - - + -
800D VAL* 3.6 18.8 - - + +
881D TYR* 3.6 25.4 - + - -
885D ILE* 3.6 25.8 - - + -
889D MET* 4.7 0.2 - - + -
924D VAL* 4.2 21.3 - - + -
927D VAL* 3.6 34.8 - - + -
945D LEU* 3.0 28.0 + - + +
948D GLU* 1.3 76.3 - - + +
950D SER* 1.3 60.1 + - - +
952D MET* 3.2 21.9 + - - +
953D ALA* 3.0 27.2 + - - +
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Residues in contact with SER 950 (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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804B LYS* 5.9 3.3 - - - -
800D VAL* 3.6 21.1 - - - +
804D LYS* 5.7 1.8 - - - -
946D ALA 2.9 21.7 + - - -
947D ALA* 3.9 7.6 - - - -
949D PHE* 1.3 78.2 - - - +
951D ARG* 1.3 60.5 + - - +
953D ALA* 3.3 17.6 + - - +
954D ARG* 3.6 13.4 + - - +
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Residues in contact with ARG 951 (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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923D ASP* 5.4 3.8 + - - -
947D ALA 3.4 11.5 + - - +
948D GLU* 2.8 50.9 + - - +
950D SER* 1.3 75.2 - - - +
952D MET* 1.3 66.3 + - - +
953D ALA 3.3 0.2 - - - -
954D ARG* 3.5 42.9 + - - +
955D ASP* 4.1 3.5 + - - +
958D ARG* 4.9 3.8 - - - +
959D TYR* 2.9 44.1 + - - -
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Residues in contact with MET 952 (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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796D LEU* 3.4 18.1 - - + +
923D ASP* 4.1 18.8 - - + +
924D VAL* 3.7 30.5 - - + -
927D VAL* 4.6 2.9 - - + -
948D GLU* 3.4 38.1 - - + +
949D PHE* 3.2 24.3 + - - +
951D ARG* 1.3 80.9 - - + +
953D ALA* 1.3 57.7 + - - +
954D ARG 3.2 0.7 - - - -
955D ASP 3.1 27.2 - - - +
956D PRO 3.2 1.7 - - - -
959D TYR* 3.6 46.9 - - + -
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Residues in contact with ALA 953 (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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793D GLN* 3.4 37.7 + - - +
796D LEU* 4.2 14.6 - - + +
797D ASN* 3.9 11.2 - - - +
800D VAL* 4.8 5.4 - - + -
949D PHE 3.0 12.4 + - - +
950D SER* 3.4 14.6 - - - +
951D ARG 3.3 0.4 - - - -
952D MET* 1.3 76.0 - - - +
954D ARG* 1.3 60.1 + - - +
955D ASP 3.2 1.3 - - - -
956D PRO* 3.4 4.1 - - - +
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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