Contacts of the helix formed by residues 100 - 113 (chain P) 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 HIS 100 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37B C 3.4 26.7 + - - -
38B C 3.1 44.0 + - - -
48B U 3.6 32.5 + - - +
49B C 4.2 2.1 + - - -
98P GLN* 3.1 16.8 + - + +
99P TYR* 1.3 76.9 + - - +
101P GLY* 1.3 80.6 + - - +
102P ARG 3.3 0.5 + - - -
103P VAL* 3.2 11.3 + - - +
104P GLN* 3.1 33.2 + - - +
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Residues in contact with GLY 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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37B C 4.8 0.2 - - - -
49B C 3.5 18.2 - - - -
68P LYS* 4.1 16.0 - - - +
100P HIS* 1.3 91.8 + - - +
102P ARG* 1.3 64.9 + - - -
104P GLN* 3.5 5.9 + - - +
105P ALA* 2.9 22.5 + - - +
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Residues in contact with ARG 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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49B C 2.7 25.4 + - - +
50B A 4.3 7.5 + - - +
30P ARG* 3.6 32.7 - - - +
31P THR 3.0 32.2 + - - -
32P PRO* 3.8 11.1 + - - +
34P HIS 3.6 9.3 + - - -
35P ILE* 4.6 10.8 - - + +
66P GLY* 2.9 41.2 + - - -
67P ASN 3.6 26.0 - - - +
68P LYS* 4.0 11.9 - - + +
71P ALA* 3.2 19.5 - - + +
101P GLY* 1.3 70.2 - - - -
103P VAL* 1.3 63.9 + - - +
105P ALA 3.0 2.6 + - - -
106P LEU* 2.9 20.5 + - - +
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Residues in contact with VAL 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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49B C 5.3 0.7 - - - +
28P VAL* 3.7 33.9 - - + -
30P ARG* 3.9 36.1 - - + +
35P ILE* 5.1 1.3 - - + -
92P PHE* 4.0 13.9 - - + -
94P ARG* 4.5 7.2 - - + -
97P PHE* 4.1 9.2 - - + +
98P GLN 3.8 20.0 - - - +
99P TYR* 4.7 4.3 - - + -
100P HIS 3.2 7.6 + - - +
102P ARG* 1.3 73.7 - - + +
104P GLN* 1.3 58.9 + - - +
106P LEU* 3.3 8.7 + - - +
107P ALA* 3.0 26.9 + - - +
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Residues in contact with GLN 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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2376A A 4.9 3.2 + - - -
99P TYR* 3.4 45.0 + - + +
100P HIS* 3.1 43.7 + - - +
101P GLY 3.5 5.1 + - - +
103P VAL* 1.3 77.3 - - - +
105P ALA* 1.3 65.4 + - - +
107P ALA* 3.2 2.4 + - - +
108P ASP* 2.9 35.0 + - - +
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Residues in contact with ALA 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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68P LYS* 4.0 20.6 - - + +
71P ALA* 3.8 14.1 - - + -
72P ALA* 4.5 5.0 - - + +
101P GLY 2.9 12.9 + - - +
102P ARG* 3.2 11.4 - - - +
104P GLN* 1.3 75.3 - - - +
106P LEU* 1.3 56.9 + - - +
108P ASP* 3.4 6.3 + - - +
109P ALA* 3.0 29.5 + - - +
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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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26P LEU* 4.6 8.3 - - + -
28P VAL* 4.2 19.7 - - + -
35P ILE* 3.5 27.1 - - + -
37P ALA* 4.5 15.3 - - + -
71P ALA* 3.3 20.3 - - + +
74P VAL* 3.6 26.5 - - + -
75P GLY* 3.7 11.4 - - - -
78P VAL* 5.1 1.8 - - + -
92P PHE* 4.3 15.3 - - + -
102P ARG 2.9 10.8 + - - +
103P VAL* 3.4 10.3 - - - +
104P GLN 3.2 0.2 - - - -
105P ALA* 1.3 73.6 - - - +
107P ALA* 1.3 68.0 + - - +
109P ALA* 3.0 3.8 + - - +
110P ALA* 3.0 20.7 + - + +
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Residues in contact with ALA 107 (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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2376A A 5.2 0.2 - - + -
92P PHE* 3.9 20.4 - - + -
99P TYR* 3.5 35.0 - - + +
103P VAL 3.0 10.8 + - - +
104P GLN 3.2 1.5 + - - +
106P LEU* 1.3 76.8 - - - +
108P ASP* 1.3 59.6 + - - +
110P ALA* 3.4 0.6 + - - -
111P ARG* 3.0 17.2 + - - +
117P PHE* 3.0 37.4 - - + -
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Residues in contact with ASP 108 (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* 3.6 3.7 + - - -
104P GLN* 2.9 35.6 + - - +
105P ALA* 3.8 5.7 - - - +
107P ALA* 1.3 74.8 - - - +
109P ALA* 1.3 59.5 + - - +
111P ARG* 3.6 28.9 + - - +
112P GLU* 2.9 38.8 + - + +
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Residues in contact with ALA 109 (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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72P ALA* 3.3 35.7 - - + +
75P GLY* 3.9 1.1 - - - -
76P LYS* 3.5 14.8 - - + +
105P ALA 3.0 17.0 + - - +
106P LEU 3.0 4.2 + - - +
108P ASP* 1.3 77.0 - - - +
110P ALA* 1.3 58.1 + - - +
112P GLU* 3.7 7.4 - - - +
113P ALA* 3.1 28.2 + - - +
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Residues in contact with ALA 110 (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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26P LEU* 4.6 10.5 - - + -
75P GLY* 3.9 9.1 - - - +
78P VAL* 5.1 1.6 - - + -
79P ALA* 3.6 22.0 - - + +
106P LEU* 3.0 15.2 + - + +
107P ALA 3.8 0.4 - - - +
109P ALA* 1.3 75.6 - - - +
111P ARG* 1.3 64.3 + - - +
113P ALA 3.2 5.9 + - - -
114P GLY 3.5 0.2 + - - -
115P LEU* 3.1 30.1 + - + +
117P PHE* 3.5 22.7 - - + -
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Residues in contact with ARG 111 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2376A A 3.1 47.5 + - - -
2377A A 3.7 6.7 + - - -
99P TYR* 2.7 29.7 + - - -
107P ALA* 3.0 18.4 + - - +
108P ASP* 3.6 20.7 + - - +
110P ALA* 1.3 75.2 - - - +
112P GLU* 1.3 62.1 + - - +
114P GLY* 3.3 11.4 + - - -
115P LEU 3.4 13.9 - - - +
117P PHE* 3.1 55.6 + - + +
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Residues in contact with GLU 112 (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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108P ASP* 2.9 27.7 + - + +
109P ALA* 3.7 8.7 - - - +
111P ARG* 1.3 80.2 - - + +
113P ALA* 1.3 56.7 + - + +
114P GLY* 3.1 5.2 + - - -
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Residues in contact with ALA 113 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76P LYS* 4.2 20.9 - - + +
79P ALA* 3.5 21.8 - - + -
80P GLU* 4.8 7.0 + - + +
83P LEU* 3.2 20.5 - - - +
109P ALA 3.1 18.8 + - - +
110P ALA 3.2 0.2 + - - -
111P ARG 3.2 1.0 - - - -
112P GLU* 1.3 75.3 - - - +
114P GLY* 1.3 57.0 + - - +
115P LEU 3.5 1.8 - - - -
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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