Contacts of the helix formed by residues 1002 - 1020 (chain C) in PDB entry 4UVL
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 ASN1002 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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952C GLY* 3.4 17.1 - - - +
953C THR* 2.8 37.7 + - + +
1000C VAL* 5.4 1.6 - - + -
1001C CYS* 1.3 73.9 - - - +
1003C LYS* 1.3 58.5 + - - +
1004C LYS* 3.2 13.6 + - - +
1005C LEU* 3.0 37.2 + - + +
1006C TRP* 2.9 31.7 + - - +
1040C ILE 4.9 1.1 - - - +
1041C HIS 3.9 11.1 + - - -
1148C TYR* 3.0 11.4 + - + +
2166C PEG 3.8 4.2 - - - -
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Residues in contact with LYS1003 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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952C GLY 4.8 2.0 + - - -
1002C ASN* 1.3 73.6 + - - +
1004C LYS* 1.3 58.4 + - - +
1006C TRP* 3.3 4.7 + - + +
1007C GLU* 3.0 62.1 + - + +
2166C PEG 3.6 21.5 + - - +
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Residues in contact with LYS1004 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1002C ASN* 3.2 8.4 + - - +
1003C LYS* 1.3 81.3 - - - +
1005C LEU* 1.3 63.4 + - + +
1007C GLU* 3.3 11.3 + - - +
1008C ARG* 3.0 51.9 + - - +
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Residues in contact with LEU1005 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1000C VAL* 6.2 0.7 - - + -
1002C ASN* 3.0 26.6 + - + +
1004C LYS* 1.3 82.4 - - + +
1006C TRP* 1.3 58.8 + - - +
1008C ARG* 3.3 40.1 + - - +
1009C TYR* 3.0 27.2 + - - +
1039C ILE 4.2 0.9 - - - +
1040C ILE 3.9 19.7 - - - +
1041C HIS 4.0 6.1 - - - +
1042C LYS* 3.6 13.0 - - - +
1043C GLY* 3.5 29.4 - - - +
1148C TYR* 3.9 19.0 - - + -
1149C PRO* 5.3 5.8 - - + -
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Residues in contact with TRP1006 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1002C ASN 2.9 19.3 + - - +
1003C LYS* 3.6 7.0 - - + +
1005C LEU* 1.3 77.2 - - - +
1007C GLU* 1.3 59.1 + - + +
1009C TYR* 3.1 23.2 + + - +
1010C THR* 2.8 56.9 + - + +
1013C ARG* 4.3 11.0 - - - -
1100C ARG* 3.8 32.3 - - - -
1148C TYR* 3.6 35.6 - + + -
2166C PEG 3.8 36.9 - - - +
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Residues in contact with GLU1007 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1003C LYS* 3.0 50.8 + - + +
1004C LYS* 3.7 10.0 - - - +
1006C TRP* 1.3 79.3 - - + +
1008C ARG* 1.3 59.2 + - - +
1010C THR* 3.1 9.8 + - - +
1011C HIS* 2.9 32.8 + - - +
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Residues in contact with ARG1008 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1004C LYS* 3.0 42.1 + - + +
1005C LEU* 3.3 33.7 - - - +
1007C GLU* 1.3 76.6 - - - +
1009C TYR* 1.3 61.1 + - - +
1011C HIS* 3.8 6.0 + - - +
1012C ARG* 3.2 23.2 + - - +
1042C LYS 3.6 12.3 + - - -
1043C GLY* 5.0 1.8 - - - -
1044C PHE 5.4 5.1 + - - -
1144C GLY 5.9 0.7 - - - -
1145C GLU* 3.7 31.4 - - + +
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Residues in contact with TYR1009 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1005C LEU 3.0 14.7 + - - +
1006C TRP* 3.1 26.0 + + - +
1008C ARG* 1.3 75.5 - - - +
1010C THR* 1.3 60.6 + - - +
1012C ARG* 3.2 4.0 + - - +
1013C ARG* 2.8 37.5 + - - +
1026C GLU* 2.5 38.9 + - - +
1100C ARG* 3.5 28.5 - - + +
1101C VAL 3.7 0.3 - - - -
1102C THR* 2.8 27.1 + - - -
1145C GLU* 3.4 21.1 - - - +
1146C GLN* 3.5 21.5 - - - -
1147C ALA 3.7 15.3 - - - +
1148C TYR* 3.8 13.2 - - + -
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Residues in contact with THR1010 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1006C TRP* 2.8 60.6 + - + +
1007C GLU* 3.1 18.0 + - - +
1009C TYR* 1.3 69.5 - - + +
1011C HIS* 1.3 63.8 + - - +
1013C ARG* 3.6 28.5 + - - +
1014C LYS* 3.1 23.4 + - - +
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Residues in contact with HIS1011 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007C GLU 2.9 19.4 + - - +
1008C ARG* 3.8 6.5 + - - +
1010C THR* 1.3 78.7 + - - +
1012C ARG* 1.3 62.0 + - - +
1014C LYS* 3.3 10.6 + - + +
1015C GLU* 3.2 50.2 + - + +
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Residues in contact with ARG1012 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1008C ARG 3.2 9.4 + - - +
1009C TYR 3.7 1.3 - - - +
1011C HIS* 1.3 80.6 + - - +
1013C ARG* 1.3 64.4 + - - +
1015C GLU* 3.2 36.1 + - - +
1016C VAL* 2.9 36.0 + - - +
1019C GLU* 4.8 9.7 + - - -
1123C HIS* 4.1 14.1 - - - +
1143C ARG* 3.3 42.5 - - + +
1145C GLU* 3.7 28.5 - - + +
1146C GLN* 3.0 46.9 + - + +
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Residues in contact with ARG1013 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1006C TRP* 4.3 9.3 - - - -
1009C TYR* 2.8 26.3 + - + +
1010C THR* 3.6 32.1 + - - +
1011C HIS 3.3 0.2 - - - -
1012C ARG* 1.3 78.0 - - - +
1014C LYS* 1.3 57.1 + - - +
1016C VAL* 3.4 1.7 + - - +
1017C SER* 2.8 32.6 + - - -
1024C ALA* 3.8 19.8 - - + +
1026C GLU* 2.8 47.1 + - - -
1100C ARG* 4.2 7.5 - - - +
1102C THR* 3.5 26.9 - - - +
1146C GLN* 6.1 0.2 - - - +
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Residues in contact with LYS1014 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010C THR 3.1 17.5 + - - +
1011C HIS* 3.7 8.7 - - + +
1012C ARG 3.2 0.2 - - - -
1013C ARG* 1.3 74.9 - - - +
1015C GLU* 1.3 63.9 + - + +
1017C SER* 3.4 6.4 + - - -
1018C GLU* 2.8 60.0 + - - +
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Residues in contact with GLU1015 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1011C HIS* 3.2 36.9 + - + +
1012C ARG* 3.2 40.9 + - - +
1014C LYS* 1.3 79.3 - - - +
1016C VAL* 1.3 57.3 + - - +
1018C GLU* 3.4 6.5 + - - +
1019C GLU* 3.0 40.1 + - - +
1143C ARG* 4.8 4.9 + - - -
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Residues in contact with VAL1016 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1012C ARG* 2.9 48.8 + - - +
1013C ARG 3.8 0.4 - - - +
1015C GLU* 1.3 75.7 - - - +
1017C SER* 1.3 59.2 + - - +
1019C GLU* 3.2 3.2 + - - +
1020C ASN* 2.8 28.9 + - + +
1024C ALA 4.4 1.6 - - - +
1102C THR* 3.6 21.3 - - + -
1104C GLY* 3.4 32.3 - - - -
1123C HIS* 3.8 21.5 - - + -
1146C GLN* 3.8 16.2 - - + +
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Residues in contact with SER1017 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1013C ARG* 2.8 20.2 + - - -
1014C LYS* 3.6 8.7 - - - -
1016C VAL* 1.3 76.7 - - - +
1018C GLU* 1.3 55.7 + - - +
1020C ASN 3.2 1.4 + - - -
1021C HIS 3.2 5.9 + - - -
1022C ASN* 2.6 39.3 + - - -
1023C HIS 3.3 25.6 + - - -
1024C ALA* 3.7 14.4 + - - +
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Residues in contact with GLU1018 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1014C LYS* 2.8 58.8 + - + +
1015C GLU* 3.9 5.5 - - - +
1017C SER* 1.3 75.7 - - - +
1019C GLU* 1.3 63.1 + - + +
1021C HIS* 3.2 15.9 + - - -
1022C ASN* 4.0 18.5 + - - +
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Residues in contact with GLU1019 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1012C ARG* 4.8 10.6 + - - -
1015C GLU* 3.0 25.8 + - - +
1016C VAL* 3.7 3.9 - - - +
1018C GLU* 1.3 76.5 - - - +
1020C ASN* 1.3 57.1 + - - +
1021C HIS* 3.3 18.1 + - - -
1123C HIS* 2.8 32.8 + - + +
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Residues in contact with ASN1020 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1016C VAL 2.8 19.1 + - - +
1017C SER 3.3 2.9 - - - -
1018C GLU 3.2 0.4 - - - -
1019C GLU* 1.3 71.1 - - - +
1021C HIS* 1.3 79.6 + - - +
1022C ASN 3.5 0.2 + - - -
1023C HIS* 2.8 50.8 + - - +
1104C GLY* 3.5 16.9 + - - -
1105C LYS* 3.5 32.1 - - - +
1123C HIS* 4.2 11.7 - - + -
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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