Contacts of the helix formed by residues 1069 - 1080 (chain C) in PDB entry 5UH8
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 GLY1069 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1067C ARG* 3.3 29.5 + - - -
1068C PHE* 1.3 77.5 - - - +
1070C GLU* 1.3 65.2 - - - -
1071C MET 3.2 2.7 - - - -
1072C GLU* 3.0 18.1 + - - -
1073C CYS* 3.0 20.4 + - - -
418D LEU 4.0 3.1 - - - -
419D GLY* 4.2 1.6 - - - -
16G C 3.6 6.3 + - - -
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Residues in contact with GLU1070 (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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1067C ARG* 4.4 3.6 - - - +
1069C GLY* 1.3 72.1 - - - -
1071C MET* 1.3 63.4 + - + +
1073C CYS* 3.3 7.4 + - + +
1074C TRP* 3.1 54.5 + - + +
414D ARG* 4.1 20.8 + - - +
418D LEU* 3.4 42.3 + - + +
419D GLY* 4.3 1.6 - - - -
875D ARG* 2.6 39.0 + - - -
1249D LYS* 4.6 4.5 + - - -
15G T 5.2 8.6 + - - +
16G C 4.7 1.0 + - - -
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Residues in contact with MET1071 (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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1069C GLY 3.2 0.6 - - - -
1070C GLU* 1.3 78.7 - - + +
1072C GLU* 1.3 73.1 + - - +
1074C TRP* 3.6 34.0 + - + +
1075C ALA* 3.6 14.0 + - - +
502D PRO* 4.7 2.2 - - + -
503D THR* 3.6 35.4 - - - +
504D LEU* 4.4 19.5 - - + -
871D GLY* 4.2 26.7 - - - +
874D THR* 5.5 2.5 - - + -
1001D GLN* 5.3 0.2 + - - -
14G G 4.0 25.1 - - + +
15G T 3.9 30.6 + - - +
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Residues in contact with GLU1072 (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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1067C ARG 5.0 0.9 - - - +
1068C PHE* 3.6 37.3 - - + -
1069C GLY* 3.0 29.6 + - - +
1071C MET* 1.3 80.9 + - - +
1073C CYS* 1.3 64.7 + - - +
1075C ALA* 3.3 5.7 + - - +
1076C MET 3.2 16.3 + - - -
499D ASN* 3.5 25.7 + - - +
501D ALA* 4.3 10.7 - - - +
503D THR* 2.5 33.2 + - - +
509D ILE* 4.0 7.6 - - + -
15G T 4.5 7.1 - - - +
16G C 4.6 8.7 - - - +
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Residues in contact with CYS1073 (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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1068C PHE* 4.1 17.7 - - - -
1069C GLY 3.0 12.3 + - - -
1070C GLU* 3.3 10.1 + - + +
1072C GLU* 1.3 77.6 - - - +
1074C TRP* 1.3 63.6 + - + +
1076C MET* 3.1 7.6 + - - +
1077C GLN* 3.0 36.7 + - - +
1085C LEU* 4.2 10.5 - - + +
1089C LEU* 4.0 25.4 - - - -
418D LEU* 3.3 24.9 - - - +
1252D VAL* 5.2 4.9 - - + -
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Residues in contact with TRP1074 (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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1070C GLU* 3.1 49.3 + - + +
1071C MET* 3.7 39.5 - - + +
1072C GLU 3.2 0.2 - - - -
1073C CYS* 1.3 76.9 - - + +
1075C ALA* 1.3 52.5 + - - +
1077C GLN* 3.1 21.2 + - - +
1078C ALA* 2.7 32.2 + - - +
503D THR 5.3 3.1 - - - -
504D LEU 5.4 1.6 - - - -
874D THR* 4.0 23.1 - - + -
875D ARG* 3.4 34.8 - - + -
878D VAL* 3.8 34.3 - - + +
882D GLN* 5.1 2.8 - - - +
997D ILE* 4.0 8.2 - - + +
1001D GLN* 3.3 24.6 + - + +
1249D LYS* 5.5 3.0 - - - +
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Residues in contact with ALA1075 (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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1071C MET 3.6 2.7 + - - +
1072C GLU 3.3 9.8 + - - +
1073C CYS 3.3 0.2 - - - -
1074C TRP* 1.3 79.2 - - - +
1076C MET* 1.3 64.1 + - - +
1079C TYR* 3.3 27.9 + - - +
503D THR* 3.7 29.4 - - + +
505D HIS 4.6 0.4 - - - +
506D ARG* 3.8 21.9 - - - +
509D ILE* 4.0 12.8 - - + -
1001D GLN* 3.5 10.2 - - - +
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Residues in contact with MET1076 (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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1068C PHE* 3.5 36.8 - - + -
1072C GLU 3.2 4.4 + - - -
1073C CYS 3.1 10.7 + - - +
1074C TRP 3.1 0.4 - - - -
1075C ALA* 1.3 76.9 - - - +
1077C GLN* 1.3 65.5 + - - +
1079C TYR* 3.0 10.0 + - + +
1080C GLY 2.9 17.3 + - - -
1081C ALA* 3.6 17.5 + - - +
1084C THR* 4.5 17.3 - - - -
1085C LEU* 4.0 28.5 - - + -
1088C LEU* 4.9 0.4 - - + -
497D LEU* 4.4 4.9 - - + -
509D ILE* 3.6 36.8 - - + -
559D MET* 3.6 23.8 - - + +
1258D ILE* 5.6 0.4 - - - -
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Residues in contact with GLN1077 (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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1073C CYS* 3.0 33.7 + - - +
1074C TRP* 3.6 21.7 - - - +
1076C MET* 1.3 74.9 - - - +
1078C ALA* 1.3 59.7 + - - +
1080C GLY* 2.8 21.8 + - - +
1085C LEU* 3.8 16.6 - - + -
882D GLN* 3.7 9.4 + - - +
994D ALA* 3.6 15.3 - - + +
997D ILE* 3.3 27.2 - - + +
1248D LEU* 3.3 27.6 - - + +
1249D LYS* 6.3 0.2 - - - +
1252D VAL* 4.7 12.9 - - - +
1258D ILE* 3.9 19.2 - - + +
1260D ALA* 5.4 0.3 - - - +
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Residues in contact with ALA1078 (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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1074C TRP 2.7 19.5 + - - +
1075C ALA 3.9 0.2 - - - +
1077C GLN* 1.3 74.0 - - - +
1079C TYR* 1.3 59.0 + - - +
506D ARG* 3.0 33.8 + - + -
993D GLU* 4.8 3.3 - - - +
994D ALA* 4.6 7.0 + - - -
997D ILE* 4.6 3.0 - - + +
998D VAL* 3.7 26.0 - - + +
1001D GLN* 3.3 29.2 - - - +
51E TYR* 4.6 3.3 + - - -
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Residues in contact with TYR1079 (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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1075C ALA 3.3 14.1 + - - +
1076C MET* 3.0 13.8 + - + +
1078C ALA* 1.3 78.3 - - - +
1080C GLY* 1.3 60.2 + - - +
1081C ALA* 3.4 6.7 - - + +
506D ARG* 3.2 46.6 + - + +
507D LEU* 3.3 16.1 - - - +
509D ILE* 3.2 26.0 + - + -
510D GLN* 4.0 6.2 - - - +
558D LEU* 4.2 16.2 - - + +
559D MET* 3.5 45.7 - - + -
564D ASN* 3.5 28.3 + - - -
51E TYR* 3.3 22.2 + - - -
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Residues in contact with GLY1080 (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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1076C MET 2.9 1.8 + - - -
1077C GLN* 2.8 17.8 + - - -
1079C TYR* 1.3 80.2 - - - +
1081C ALA* 1.3 61.6 + - - +
1082C ALA* 3.2 6.9 + - - -
558D LEU* 4.1 2.3 - - - +
992D GLY 5.6 0.4 - - - -
994D ALA* 5.9 1.8 - - - -
1258D ILE* 5.4 2.2 - - - -
1260D ALA* 4.9 2.9 - - - -
1261D GLY* 3.6 11.3 - - - -
1262D THR* 3.3 25.1 + - - +
51E TYR* 3.8 16.5 - - - -
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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