Contacts of the helix formed by residues 548 - 557 (chain D) 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 SER 548 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1083C TYR* 4.9 6.2 + - - +
1087C GLU* 2.9 17.7 + - - +
1091C ILE* 5.4 0.9 - - - -
1112C ILE* 3.5 29.6 - - - -
547D LEU* 1.3 81.6 - - - +
549D ALA* 1.3 66.2 + - - +
550D GLU* 3.5 13.8 + - - +
551D ALA* 2.9 34.8 + - - +
552D GLN* 3.3 6.2 + - - +
62E ARG* 4.6 2.2 - - - -
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Residues in contact with ALA 549 (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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1111C ASN* 6.4 0.2 - - - -
1112C ILE* 4.8 2.6 - - - +
547D LEU 3.7 1.3 + - - -
548D SER* 1.3 74.3 - - - +
550D GLU* 1.3 63.1 + - - +
552D GLN* 3.5 7.7 + - - +
553D ALA* 3.5 14.0 + - - +
58E ALA* 3.7 19.8 - - + +
61E ALA* 4.8 8.5 - - + -
62E ARG* 3.9 37.0 - - + +
92E LEU* 3.9 9.6 - - - +
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Residues in contact with GLU 550 (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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1083C TYR* 3.8 41.5 - - + -
548D SER* 3.5 11.3 + - - -
549D ALA* 1.3 71.0 - - - +
551D ALA* 1.3 60.7 + - - +
553D ALA* 3.0 4.8 + - - +
554D GLU* 2.8 32.3 + - - +
54E VAL* 4.0 2.6 - - + +
55E ILE* 4.1 20.6 - - + -
58E ALA* 3.6 21.2 - - + +
59E LYS* 5.3 8.1 - - + +
62E ARG* 3.0 42.6 + - - -
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Residues in contact with ALA 551 (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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1083C TYR* 4.8 0.2 - - - +
1084C THR* 3.3 31.4 + - - +
1087C GLU* 4.2 8.5 - - - +
546D PRO* 3.8 18.8 - - + +
547D LEU 4.2 1.6 - - - +
548D SER* 2.9 29.0 + - - +
550D GLU* 1.3 79.5 - - - +
552D GLN* 1.3 57.8 + - - +
554D GLU* 3.3 3.1 + - - -
555D ALA* 3.0 27.7 + - - +
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Residues in contact with GLN 552 (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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455D PHE* 5.9 1.2 - - - -
493D GLU 5.4 1.0 - - - +
494D HIS* 3.7 35.3 + - + +
495D PRO* 4.1 13.6 - - + +
546D PRO* 4.1 15.7 - - + +
547D LEU 2.9 23.7 + - - +
548D SER 3.5 10.3 + - - +
549D ALA* 4.0 5.5 - - - +
550D GLU 3.3 0.6 - - - -
551D ALA* 1.3 75.4 - - - +
553D ALA* 1.3 57.5 + - - +
555D ALA* 3.4 7.7 - - - +
556D ARG* 2.8 32.6 + - - +
90E LYS* 5.5 6.8 - - - +
91E PRO* 6.2 0.3 - - - +
92E LEU* 3.5 25.8 - - + +
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Residues in contact with ALA 553 (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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549D ALA 3.5 10.3 + - - +
550D GLU 3.0 10.2 + - - +
552D GLN* 1.3 77.1 - - - +
554D GLU* 1.3 63.0 + - - +
555D ALA 3.1 0.2 - - - -
556D ARG* 4.9 1.6 - - - -
557D ILE* 3.1 38.5 + - + +
54E VAL* 3.6 31.4 - - + +
57E ALA* 4.9 2.7 - - + -
58E ALA* 4.2 7.4 - - + +
92E LEU* 3.5 14.8 - - + +
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Residues in contact with GLU 554 (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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1081C ALA* 3.1 20.8 - - + -
1082C ALA 3.1 4.3 + - - -
1083C TYR* 3.0 26.2 + - - +
1084C THR* 2.5 48.6 + - - +
550D GLU 2.8 14.6 + - - +
551D ALA* 3.7 2.0 - - - +
553D ALA* 1.3 76.2 - - - +
555D ALA* 1.3 57.7 + - - +
558D LEU* 3.2 41.4 + - + +
559D MET* 3.2 10.5 - - - +
1262D THR* 2.9 24.8 + - + +
54E VAL* 3.6 15.5 - - + -
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Residues in contact with ALA 555 (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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1084C THR* 5.7 0.7 - - + +
495D PRO* 4.0 19.7 - - + -
497D LEU* 4.6 8.5 - - + -
511D ALA* 3.3 17.6 - - + +
546D PRO* 4.4 10.1 - - + -
551D ALA 3.0 16.4 + - - +
552D GLN* 3.4 6.7 - - - +
553D ALA 3.1 0.4 - - - -
554D GLU* 1.3 77.6 - - - +
556D ARG* 1.3 61.0 + - - +
559D MET* 3.5 11.3 + - - -
560D LEU* 3.1 26.2 + - - -
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Residues in contact with ARG 556 (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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493D GLU* 3.9 27.1 + - - -
495D PRO* 4.6 5.4 - - + +
552D GLN 2.8 19.8 + - - +
553D ALA* 4.4 2.5 - - - +
555D ALA* 1.3 74.8 - - - +
557D ILE* 1.3 64.4 + - - +
560D LEU* 3.1 30.8 - - + +
563D ASN* 3.7 3.3 + - - -
35E ILE* 3.0 61.3 + - + +
37E ASN 3.4 18.2 + - - -
38E PRO* 4.7 0.4 + - - +
40E ILE* 5.2 0.3 - - - +
92E LEU* 3.6 20.1 - - + +
93E SER* 4.1 20.4 + - - +
96E LEU* 3.6 29.4 - - - +
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Residues in contact with ILE 557 (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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553D ALA* 3.1 23.3 + - + +
556D ARG* 1.3 91.3 - - + +
558D LEU* 1.3 75.4 + - + +
560D LEU 4.5 0.2 - - - -
563D ASN* 2.9 25.4 + - - +
40E ILE* 3.7 22.6 - - + +
43E LEU* 6.1 0.9 - - + -
50E LYS* 4.3 17.0 + - + +
53E LEU* 3.6 38.8 - - + +
54E VAL* 3.8 21.1 - - + -
57E ALA* 5.0 0.4 - - + -
96E LEU* 4.5 15.0 - - + -
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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