Contacts of the helix formed by residues 98 - 106 (chain P) in PDB entry 5G04
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 GLU 98 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53C LYS* 4.4 5.2 + - - +
295C TYR 5.5 1.8 - - - +
297C ILE* 5.7 4.7 - - + -
326C ILE* 6.4 1.8 - - + -
327C ASP* 6.6 0.2 - - - -
330C ARG* 4.6 19.5 + - - +
93P TYR* 3.0 40.6 + - + +
96P VAL* 3.6 26.8 - - - +
97P LYS* 1.3 71.0 + - - +
99P TYR* 1.3 64.7 + - - +
100P ASP* 3.4 1.8 - - + +
101P ARG* 3.3 37.7 + - + +
102P ALA* 3.2 18.2 + - - +
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Residues in contact with TYR 99 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5M VAL* 4.2 15.9 - - - +
94P PHE* 3.6 52.3 - + - -
97P LYS* 3.5 36.9 + - + +
98P GLU* 1.3 71.7 - - - +
100P ASP* 1.3 67.7 + - - +
102P ALA* 3.3 6.5 + - - +
103P ALA* 3.0 22.7 + - - +
121P SER* 3.7 19.3 - - - +
124P LEU* 3.8 25.5 - - + +
125P SER* 3.8 11.4 - - - -
128P LYS* 3.4 43.9 + - + -
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Residues in contact with ASP 100 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295C TYR* 3.7 33.9 - - + -
325C GLU 5.1 1.7 - - - +
326C ILE* 3.7 31.5 - - + +
98P GLU* 3.4 1.0 - - + +
99P TYR* 1.3 81.4 + - - +
101P ARG* 1.3 61.4 + - - +
103P ALA* 3.2 9.2 + - - +
104P HIS 3.2 16.6 + - - -
125P SER* 3.4 27.1 + - - +
129P LYS* 4.4 13.3 + - - +
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Residues in contact with ARG 101 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C LYS* 5.7 1.4 - - - +
293C ASP* 3.0 31.6 + - - +
295C TYR* 3.4 25.1 + - + +
296C ARG* 3.2 38.5 - - - +
297C ILE* 4.0 12.3 - - - +
298C GLU* 4.4 7.3 - - - +
326C ILE* 5.7 0.2 - - - +
330C ARG* 4.2 12.1 - - - +
93P TYR* 3.3 38.7 + - + -
98P GLU* 3.3 40.0 + - + +
99P TYR 3.3 0.4 - - - -
100P ASP* 1.3 76.2 - - - +
102P ALA* 1.3 65.4 + - - +
104P HIS* 3.3 8.8 + - - +
105P PHE* 3.2 26.4 + - + -
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Residues in contact with ALA 102 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90P ALA* 3.3 32.8 - - + +
93P TYR* 4.1 4.8 - - + +
94P PHE* 3.8 17.9 - - + +
98P GLU 3.2 12.0 + - - +
99P TYR* 3.3 9.2 + - - +
101P ARG* 1.3 79.4 - - - +
103P ALA* 1.3 62.0 + - - +
105P PHE* 3.3 9.4 + - - -
106P LEU* 3.4 19.2 + - - +
117P LEU* 5.0 2.5 - - + -
121P SER* 4.5 7.2 - - - -
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Residues in contact with ALA 103 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99P TYR 3.0 10.5 + - - +
100P ASP* 3.4 12.6 - - - +
102P ALA* 1.3 75.4 - - - +
104P HIS* 1.3 62.1 + - - +
105P PHE 3.3 0.7 + - - -
106P LEU 3.3 2.1 + - - +
107P HIS* 3.3 17.1 + - - -
118P TYR* 3.4 30.0 - - + +
121P SER* 3.4 22.8 + - - +
122P ARG* 4.5 13.9 - - + +
125P SER* 5.6 0.2 - - - +
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Residues in contact with HIS 104 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291C LYS 5.8 1.8 - - - -
292C GLN 3.9 13.5 + - - -
293C ASP* 4.0 2.0 - - - -
294C PRO* 3.3 39.9 - - + +
295C TYR* 3.4 28.1 - - + -
100P ASP 3.2 3.6 + - - -
101P ARG 3.5 5.2 - - - +
103P ALA* 1.3 79.5 - - - +
105P PHE* 1.3 93.0 + + - +
107P HIS* 3.4 27.4 - - - +
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Residues in contact with PHE 105 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C GLU* 4.5 8.7 - - - -
60C PHE* 4.2 26.2 - + - -
263C SER* 5.6 3.4 - - - -
292C GLN 5.0 4.0 - - - -
293C ASP* 3.8 23.1 - - + -
86P ALA* 4.3 16.6 - - - +
89P LEU* 3.7 38.4 - - + -
90P ALA* 4.4 12.3 - - + -
93P TYR* 3.9 13.0 - + - -
101P ARG* 3.2 41.4 + - + -
102P ALA* 3.3 6.5 + - - +
103P ALA 3.2 0.8 - - - -
104P HIS* 1.3 96.3 - + - +
106P LEU* 1.3 61.7 + - - +
107P HIS 3.2 0.7 + - - -
108P GLY 4.4 3.5 + - - -
109P CYS* 5.3 0.5 + - - +
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Residues in contact with LEU 106 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83P ASP* 6.2 0.2 - - + -
86P ALA* 4.3 2.5 - - + +
87P TYR* 4.0 23.3 - - + +
90P ALA* 3.4 30.1 - - + -
102P ALA 3.4 11.1 + - - +
103P ALA 3.3 2.1 + - - +
104P HIS 3.3 0.8 - - - -
105P PHE* 1.3 74.6 - - - +
107P HIS* 1.3 63.9 + - - +
108P GLY 3.1 4.4 + - - -
109P CYS* 3.1 25.3 + - + +
114P ALA* 4.1 26.1 - - + +
115P TYR* 5.9 0.2 - - - -
117P LEU* 3.7 21.1 - - + -
118P TYR* 3.5 47.6 - - + +
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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