Contacts of the helix formed by residues 97 - 107 (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 PRO 97 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59K ALA* 4.4 2.6 - - + +
60K ASP* 3.7 35.0 - - + +
92K MET 3.2 8.5 - - - +
93K ILE* 3.3 33.2 - - + +
94K ALA 4.7 0.7 - - - +
95K ARG 3.6 5.6 - - - +
96K ARG* 1.3 86.6 - - - +
98K GLU* 1.3 76.9 + - - +
100K VAL* 3.1 22.5 + - - +
101K ILE* 4.0 4.9 + - - +
126K ALA* 4.0 15.5 - - + -
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Residues in contact with GLU 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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59K ALA* 4.0 3.8 - - + -
96K ARG* 3.3 30.2 + - - +
97K PRO* 1.3 82.4 - - - +
99K ARG* 1.3 67.1 + - - +
101K ILE* 3.0 15.6 + - - +
102K GLU* 3.0 33.8 + - - +
124K VAL* 3.8 32.0 - - + +
125K TYR* 4.0 1.0 - - - -
126K ALA* 3.2 40.2 + - - +
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Residues in contact with ARG 99 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2041A U 5.9 0.4 + - - -
2639A A 5.7 5.5 + - - -
2640A G 6.0 2.7 - - - +
2780A G 4.2 11.7 + - - +
92K MET* 3.6 16.2 - - + -
96K ARG* 3.3 44.6 - - + +
98K GLU* 1.3 78.0 - - - +
100K VAL* 1.3 56.1 + - - +
102K GLU* 3.3 30.2 + - - +
103K ILE* 2.9 54.7 + - - +
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Residues in contact with VAL 100 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1139A G 4.9 0.3 + - - -
25K LEU* 3.9 24.0 - - + -
62K VAL* 4.8 4.3 - - + -
74K TYR* 4.0 10.0 + - - +
89K PHE* 3.9 32.1 - - + -
92K MET* 3.5 35.9 - - + +
93K ILE* 4.3 10.5 - - + -
97K PRO 3.1 13.6 + - - +
98K GLU 3.0 0.4 + - - -
99K ARG* 1.3 77.4 - - - +
101K ILE* 1.3 63.8 + - + +
103K ILE* 3.1 7.5 + - - +
104K ALA* 2.9 27.7 + - - +
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Residues in contact with ILE 101 (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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20K ALA* 4.6 7.4 - - + -
25K LEU* 4.6 12.8 - - + -
28K LEU* 4.6 7.9 - - + -
29K ALA* 5.9 2.0 - - + -
32K LEU* 4.3 24.0 - - + -
56K VAL* 3.9 22.2 - - + -
59K ALA* 3.5 41.1 - - + +
62K VAL* 5.1 4.5 - - + -
97K PRO 4.3 7.4 - - - +
98K GLU 3.0 7.4 + - - +
100K VAL* 1.3 81.4 - - + +
102K GLU* 1.3 63.1 + - - +
104K ALA* 3.3 0.7 + - - +
105K VAL* 2.9 29.3 + - + +
122K LEU* 5.0 5.4 - - + -
124K VAL* 4.0 9.0 - - + -
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Residues in contact with GLU 102 (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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2780A G 3.0 45.9 + - - +
96K ARG* 3.8 1.4 + - - -
98K GLU* 3.0 36.5 + - - +
99K ARG* 3.3 24.0 + - - +
101K ILE* 1.3 75.0 - - - +
103K ILE* 1.3 58.0 + - - +
105K VAL* 4.7 2.5 - - - -
106K LYS* 3.0 32.9 + - - +
119K PHE* 3.7 25.7 - - + -
122K LEU* 4.9 3.8 - - + -
124K VAL* 3.6 24.3 - - + +
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Residues in contact with ILE 103 (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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1138A G 4.3 3.4 - - - +
1139A G 3.1 20.6 - - - +
74K TYR* 4.0 27.6 - - + -
92K MET* 4.2 10.8 - - + -
99K ARG* 2.9 53.7 + - - +
100K VAL 3.3 3.4 - - - +
102K GLU* 1.3 76.2 - - - +
104K ALA* 1.3 58.8 + - - +
106K LYS* 3.2 6.9 + - + +
107K GLY* 2.9 29.1 + - - -
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Residues in contact with ALA 104 (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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1138A G 2.9 29.5 + - - -
1139A G 3.3 22.2 - - - +
25K LEU* 4.1 24.9 - - + -
29K ALA* 4.3 10.8 - - + -
100K VAL 2.9 15.6 + - - +
101K ILE 4.0 2.5 - - - +
103K ILE* 1.3 73.9 - - - +
105K VAL* 1.3 63.8 + - - +
108K MET* 3.4 13.5 - - - +
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Residues in contact with VAL 105 (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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29K ALA* 4.1 13.7 - - + +
32K LEU* 3.9 32.3 - - + -
33K ALA* 4.9 3.0 - - - +
36K LEU* 3.9 14.1 - - + -
101K ILE* 2.9 17.2 + - + +
102K GLU 4.1 1.1 - - - +
104K ALA* 1.3 75.4 - - - +
106K LYS* 1.3 58.6 + - - +
108K MET* 2.7 29.6 + - - +
109K LEU* 3.2 33.2 + - + +
119K PHE* 4.6 5.8 - - + -
122K LEU* 3.7 25.6 - - + -
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Residues in contact with LYS 106 (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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2040A G 4.2 20.3 + - - +
2041A U 3.4 27.8 + - - -
102K GLU 3.0 21.4 + - - +
103K ILE* 3.7 6.3 - - + +
105K VAL* 1.3 80.2 - - - +
107K GLY* 1.3 63.2 + - - +
109K LEU* 3.1 26.0 + - + +
111K LYS* 4.0 10.2 - - + +
119K PHE* 4.2 20.6 - - + -
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Residues in contact with GLY 107 (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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1137A G 3.3 18.3 + - - +
1138A G 3.3 30.3 - - - +
2039A U 5.0 0.7 + - - -
2040A G 5.6 5.4 - - - -
103K ILE 2.9 13.6 + - - -
105K VAL 3.1 0.2 - - - -
106K LYS* 1.3 77.9 - - - +
108K MET* 1.3 58.1 + - - +
111K LYS* 3.6 19.2 + - - -
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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