Contacts of the helix formed by residues 89 - 96 (chain K) in PDB entry 5GAG
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 PHE 89 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25K LEU* 4.3 9.9 - - + -
62K VAL* 3.9 23.6 - - + -
64K VAL* 3.7 26.9 - - + -
68K LYS 3.7 10.5 - - - +
69K ARG* 3.4 43.5 - - - +
72K LYS* 2.9 27.4 + - + +
74K TYR* 3.5 33.4 - + + -
87K ALA 3.8 0.2 + - - -
88K THR* 1.3 73.3 - - - +
90K GLU* 1.3 65.4 + - - +
92K MET* 2.9 15.5 + - - +
93K ILE* 3.0 26.8 + - + +
100K VAL* 3.9 18.8 - - + -
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Residues in contact with GLU 90 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2738A A 4.9 12.4 + - - +
69K ARG* 3.2 35.3 + - + +
70K THR* 4.6 19.4 - - - +
88K THR* 3.2 9.4 + - - +
89K PHE* 1.3 82.6 - - - +
91K GLU* 1.3 62.9 + - + +
93K ILE* 3.1 11.0 + - + +
94K ALA* 2.9 23.7 + - - +
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Residues in contact with GLU 91 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2738A A 5.6 6.1 + - - +
2767A C 5.6 1.7 + - - -
87K ALA* 3.1 14.1 - - + +
88K THR* 2.4 62.4 + - - +
90K GLU* 1.3 76.4 - - + +
92K MET* 1.3 60.0 + - - +
94K ALA* 3.5 13.1 - - + +
95K ARG* 2.9 43.4 + - - +
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Residues in contact with MET 92 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74K TYR* 4.1 28.3 - - + -
87K ALA* 4.4 13.9 - - + +
88K THR 3.3 13.1 + - - +
89K PHE* 2.9 10.9 + - - +
91K GLU* 1.3 79.0 - - - +
93K ILE* 1.3 56.6 + - - +
95K ARG* 4.9 9.0 - - - +
96K ARG 3.0 41.1 + - - +
97K PRO* 4.3 1.6 - - - -
99K ARG* 3.6 30.3 - - + -
100K VAL* 3.5 31.0 - - + +
103K ILE* 4.2 11.7 - - + -
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Residues in contact with ILE 93 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59K ALA 4.6 0.2 - - - +
60K ASP* 3.8 34.6 - - + +
62K VAL* 4.2 9.2 - - + +
69K ARG* 4.6 7.2 - - - +
89K PHE* 3.0 46.5 + - + +
90K GLU* 3.2 9.2 - - - +
92K MET* 1.3 74.1 - - - +
94K ALA* 1.3 65.7 - - - +
97K PRO* 3.3 37.8 - - + +
100K VAL* 4.3 8.1 - - + -
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Residues in contact with ALA 94 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90K GLU 2.9 8.1 + - - +
91K GLU* 3.5 20.9 - - + +
93K ILE* 1.3 81.0 - - - +
95K ARG* 1.3 62.6 + - - +
97K PRO* 4.7 0.7 - - - +
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Residues in contact with ARG 95 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2640A G 4.1 25.8 + - - +
2768A U 3.3 41.8 + - - -
2769A U 4.8 7.0 + - - -
91K GLU* 2.9 29.7 + - - +
92K MET* 4.2 8.1 - - - +
94K ALA* 1.3 78.8 - - - +
96K ARG* 1.3 70.8 + - + +
97K PRO* 3.6 5.2 - - - +
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Residues in contact with ARG 96 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2639A A 5.2 22.0 + - - -
2640A G 6.0 0.9 - - - +
2780A G 2.9 35.8 - - - +
92K MET* 3.0 13.4 + - - +
95K ARG* 1.3 90.4 - - + +
97K PRO* 1.3 65.7 - - - +
98K GLU* 3.1 31.1 + - - +
99K ARG* 3.2 44.7 + - + +
100K VAL 4.3 0.5 + - - -
102K GLU* 3.8 7.9 + - - -
124K VAL 5.5 1.2 + - - -
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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