Contacts of the helix formed by residues 91 - 98 (chain K) in PDB entry 3EXG
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 ALA 91 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87K THR* 3.6 26.2 - - + -
88K ALA 4.1 0.7 - - - +
89K TYR 3.2 5.9 + - - +
90K ARG* 1.3 72.8 - - - +
92K HIS* 1.3 64.6 + - + +
93K GLY 3.3 2.2 - - - -
94K PHE* 3.2 6.6 + - - +
95K THR* 2.8 33.4 + - - +
123K SER 5.5 1.8 + - - +
124K MET 5.0 2.7 - - - +
126K MET* 4.6 5.4 - - + +
131K PHE* 3.9 11.4 - - + -
134K GLY* 4.0 17.7 - - - +
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Residues in contact with HIS 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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45K MET* 4.6 12.3 - - - -
46K GLU* 3.2 30.2 + - - +
49K ALA* 5.4 0.4 - - - +
62K CYS* 4.4 2.7 - - - -
63K HIS 3.3 31.6 + - - -
64K LEU* 4.2 8.4 - - + +
65K CYS* 5.3 0.6 - - - +
89K TYR 5.1 1.2 + - - -
90K ARG 3.7 1.6 - - - -
91K ALA* 1.3 76.7 + - - +
93K GLY* 1.3 68.5 + - - +
95K THR* 3.0 2.8 + - - -
96K PHE* 3.0 23.6 + - - +
105K ILE* 4.1 7.1 - - + +
109K LEU* 4.1 19.8 - - + +
123K SER* 3.1 33.0 + - - -
126K MET* 3.4 30.3 - - + -
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Residues in contact with GLY 93 (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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42K VAL* 3.9 14.6 - - - -
65K CYS* 3.7 27.4 - - - +
72K CYS* 3.7 17.0 - - - -
90K ARG 5.0 0.2 + - - -
91K ALA 3.3 0.6 - - - -
92K HIS* 1.3 77.9 - - - +
94K PHE* 1.3 59.1 + - - +
96K PHE* 3.3 3.3 + - - +
97K THR* 3.0 30.3 + - - +
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Residues in contact with PHE 94 (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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65K CYS* 6.4 2.7 - - + -
68K GLN* 6.0 0.7 - - - -
71K CYS* 4.8 0.4 - - + -
72K CYS* 3.5 30.5 - - + -
75K LEU* 3.6 24.5 - - + -
85K LEU* 3.6 30.1 - - + -
87K THR* 4.6 9.9 - - + -
90K ARG 4.3 16.6 - - - -
91K ALA* 3.2 6.4 + - - +
92K HIS 3.1 0.8 - - - -
93K GLY* 1.3 75.3 - - - +
95K THR* 1.3 55.9 + - - +
97K THR* 3.1 9.4 + - - -
98K ARG* 2.7 40.9 + - + +
131K PHE* 4.0 18.2 - + + -
164K LEU* 3.1 29.8 - - + -
194K GLU* 4.1 16.8 - - - -
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Residues in contact with THR 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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91K ALA* 2.8 17.2 + - - +
92K HIS 3.0 8.0 + - - -
94K PHE* 1.3 73.6 - - - +
96K PHE* 1.3 67.3 + - - +
98K ARG* 3.5 5.9 + - - +
99K GLY 3.7 0.3 + - - -
100K LEU* 3.1 45.9 + - + +
105K ILE* 3.4 21.8 - - + -
126K MET* 3.6 26.4 - - + +
131K PHE* 3.3 25.7 - - + -
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Residues in contact with PHE 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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37K ARG* 6.2 0.9 - - + -
38K MET* 4.1 27.4 - - + -
41K THR* 3.4 38.4 - - + -
42K VAL* 3.7 22.4 - - + -
45K MET* 4.5 4.9 - - + -
92K HIS 3.0 11.5 + - - +
93K GLY 3.5 7.4 - - - +
95K THR* 1.3 75.5 - - - +
97K THR* 1.3 65.8 + - + +
98K ARG 3.0 0.2 - - - -
99K GLY* 2.8 24.4 + - - -
100K LEU 3.7 20.8 - - - +
101K SER* 5.4 0.7 - - - -
102K VAL* 3.8 25.1 - - + -
105K ILE* 3.6 9.0 - - + +
316K GLU* 6.5 0.2 - - + -
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Residues in contact with THR 97 (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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38K MET* 4.8 12.4 - - - +
42K VAL* 4.3 2.0 - - + -
72K CYS* 3.4 40.0 + - - +
73K VAL* 4.2 13.0 - - + -
76K GLU* 3.5 33.6 + - - +
93K GLY 3.0 15.9 + - - +
94K PHE* 3.1 15.1 + - - -
96K PHE* 1.3 90.9 - - + +
98K ARG* 1.3 57.4 + - - +
99K GLY 3.2 3.4 + - - -
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Residues in contact with ARG 98 (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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76K GLU* 2.9 38.9 + - - -
79K ILE* 3.7 11.2 - - - +
80K ASN 3.2 21.2 + - - -
81K PRO* 3.9 8.8 + - - +
83K ASP 2.8 21.6 + - - -
85K LEU* 3.9 22.2 - - - +
94K PHE* 2.7 19.9 + - - +
95K THR* 3.8 4.0 - - - +
96K PHE 2.8 1.0 + - - -
97K THR* 1.3 77.9 - - - +
99K GLY* 1.3 57.0 + - - +
100K LEU 3.7 2.2 - - - -
128K ALA* 3.8 12.2 - - + +
129K LYS* 3.7 12.8 + - - +
130K ASN* 2.7 40.2 + - - +
131K PHE* 3.3 32.1 - - + -
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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