Contacts of the helix formed by residues 131 - 147 (chain A) in PDB entry 2GTL
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 ASN 131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A ASP* 5.2 0.3 - - - +
14A GLU* 3.4 27.1 - - - +
18A ILE* 3.7 14.6 - - + +
129A CYS 3.9 2.4 + - - -
130A PHE* 1.3 69.7 - - - +
132A VAL* 1.3 64.3 + - - +
133A ASP* 3.6 10.9 - - - +
134A ALA* 2.8 42.9 + - + +
135A TRP* 3.0 10.8 + - - +
137A ARG* 5.2 2.1 + - - +
188M GLU* 4.2 23.4 + - - +
210M VAL* 5.0 3.9 - - - +
212M SER* 4.6 5.4 - - - -
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Residues in contact with VAL 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ALA* 4.5 20.2 - - + +
124A PRO* 5.8 2.5 - - + -
130A PHE* 2.9 36.1 + - + +
131A ASN* 1.3 70.7 - - - +
133A ASP* 1.3 75.9 + - - +
135A TRP* 3.4 1.8 + - + +
136A ASN* 2.8 46.8 + - - +
188M GLU* 4.8 14.6 - - - +
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Residues in contact with ASP 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ASN* 2.8 13.7 + - - +
132A VAL* 1.3 88.5 - - - +
134A ALA* 1.3 56.2 - - - +
136A ASN* 3.0 10.8 + - - +
137A ARG* 2.7 54.2 + - - +
187M SER* 5.3 4.5 - - - +
188M GLU* 4.9 12.1 - - + +
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Residues in contact with ALA 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASP* 3.8 19.7 - - + +
14A GLU* 4.3 15.7 - - + -
15A ILE* 3.8 9.0 - - + +
18A ILE* 5.6 0.4 - - + -
131A ASN* 2.8 38.7 + - + +
133A ASP* 1.3 75.2 - - - +
135A TRP* 1.3 65.4 + - - +
137A ARG* 3.3 16.1 + - - +
138A CYS* 3.2 18.2 + - - +
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Residues in contact with TRP 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ILE* 4.1 27.2 - - + +
18A ILE* 4.9 8.0 - - + +
19A TRP* 4.0 22.4 - + - -
77A LEU* 4.5 5.8 - - + -
81A ILE* 4.0 22.7 - - + -
116A GLY 4.9 0.4 + - - -
119A PHE* 3.9 22.5 - + + +
120A ALA* 4.6 4.0 - - - +
123A LEU* 3.6 22.4 - - + -
130A PHE* 3.4 40.6 - + + -
131A ASN* 3.0 8.3 + - - +
132A VAL 3.5 5.4 - - - +
134A ALA* 1.3 79.9 - - - +
136A ASN* 1.3 92.2 + - - +
138A CYS* 3.0 1.6 + - - +
139A PHE* 2.8 65.9 + + + +
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Residues in contact with ASN 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A GLY 4.5 5.1 + - - -
120A ALA* 3.7 26.2 - - - +
132A VAL* 2.8 33.2 + - - +
133A ASP* 3.3 10.1 - - - +
135A TRP* 1.3 82.9 - - - +
137A ARG* 1.3 64.0 + - + +
139A PHE* 3.7 3.1 - - - +
140A HIS* 2.9 49.4 + - + +
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Residues in contact with ARG 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ASP* 4.5 23.4 - - - +
6A CYS 3.7 19.1 - - - +
7A CYS* 5.0 3.0 + - - -
11A ASP* 2.6 42.4 + - - +
131A ASN* 5.2 2.0 + - - +
133A ASP* 2.7 42.0 + - - +
134A ALA* 3.6 16.2 - - - +
135A TRP 3.0 0.8 + - - -
136A ASN* 1.3 76.8 - - + +
138A CYS* 1.3 61.5 + - - +
140A HIS* 3.1 12.0 + - - +
141A ARG* 3.2 12.1 + - - +
5G HIS* 3.4 47.3 + - - -
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Residues in contact with CYS 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A CYS* 2.0 56.0 - - - -
11A ASP* 3.6 24.5 - - - -
12A ARG* 4.3 2.0 - - - -
15A ILE* 3.3 29.4 - - + -
84A LEU* 5.4 5.2 - - + -
134A ALA 3.2 0.8 + - - -
135A TRP 3.0 2.2 + - - -
137A ARG* 1.3 80.1 - - - +
139A PHE* 1.3 61.7 + - - +
141A ARG* 3.6 2.8 + - - +
142A LEU* 3.2 28.4 + - + +
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Residues in contact with PHE 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ILE* 5.2 0.4 - - - +
77A LEU* 4.2 21.1 - - + -
80A LEU* 6.3 0.4 - - + -
115A ILE* 4.6 1.3 - - + -
116A GLY* 3.4 33.2 - - - -
119A PHE* 3.8 16.4 - + - -
135A TRP* 2.8 58.1 + + + +
136A ASN* 3.7 5.2 - - - +
138A CYS* 1.3 74.4 - - - +
140A HIS* 1.3 68.2 + + - +
142A LEU* 3.1 17.2 + - + +
143A VAL* 2.8 46.7 + - + +
160A HEM 3.6 26.7 - - + -
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Residues in contact with HIS 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ASP* 6.3 3.8 - - + -
113A ARG* 5.7 7.0 - - + +
116A GLY* 5.9 6.1 - - - -
136A ASN* 2.9 44.5 + - + +
137A ARG* 3.5 9.6 - - - +
139A PHE* 1.3 81.3 - + - +
141A ARG* 1.3 66.8 + - - +
143A VAL* 3.1 7.0 + - + +
144A ALA* 2.8 28.2 + - - +
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Residues in contact with ARG 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ASP 5.4 9.0 - - - +
6A CYS* 6.0 0.4 - - - -
7A CYS* 4.4 24.7 - - + +
90A LEU* 5.3 5.8 - - - +
91A GLN* 4.4 25.3 + - - +
94A LEU* 3.7 24.8 - - - +
137A ARG 3.2 8.9 + - - +
138A CYS 3.9 7.4 - - - +
139A PHE 3.3 0.2 - - - -
140A HIS* 1.3 79.1 - - - +
142A LEU* 1.3 68.2 + - + +
144A ALA* 3.9 5.4 - - - +
145A ARG* 3.5 26.7 + - - +
134G LEU* 3.6 32.5 - - + +
137G LYS* 4.5 23.0 - - - +
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Residues in contact with LEU 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A LEU* 5.1 4.3 - - + -
80A LEU* 4.3 26.9 - - + -
81A ILE* 5.2 7.6 - - + +
84A LEU* 4.5 16.8 - - + -
90A LEU* 4.1 22.9 - - + -
94A LEU* 3.7 31.4 - - + +
138A CYS* 3.2 16.8 + - + +
139A PHE* 3.1 22.1 + - + +
140A HIS 3.0 0.4 - - - -
141A ARG* 1.3 84.5 - - - +
143A VAL* 1.3 63.5 + - + +
145A ARG* 3.6 3.1 + - - +
146A ILE* 3.0 28.2 + - + +
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Residues in contact with VAL 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A PHE* 3.9 44.4 - - + +
113A ARG* 4.7 4.5 - - + +
115A ILE* 5.4 0.2 - - + -
116A GLY* 5.5 0.9 - - - -
139A PHE* 2.8 54.0 + - + +
140A HIS* 3.7 6.7 - - + +
142A LEU* 1.3 70.4 - - + +
144A ALA* 1.3 68.8 + - - +
146A ILE* 2.7 21.8 + - + +
147A ALA* 2.9 14.0 + - + +
160A HEM 5.3 2.7 - - + -
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Residues in contact with ALA 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A LYS* 5.8 2.0 - - - +
140A HIS* 2.8 21.4 + - + +
141A ARG* 3.9 7.2 - - - +
143A VAL* 1.3 76.9 - - - +
145A ARG* 1.3 61.9 + - - +
147A ALA* 3.4 3.2 + - - -
148A LYS* 3.1 24.6 + - - +
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Residues in contact with ARG 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A GLN* 4.6 14.9 + - + +
94A LEU* 3.9 29.6 - - + +
95A GLY* 3.3 30.8 - - - -
98A ALA* 4.0 8.9 - - - +
99A ASP* 5.9 0.6 + - - -
141A ARG* 3.5 22.3 + - - +
142A LEU 4.0 3.8 - - - +
143A VAL 3.2 0.8 - - - -
144A ALA* 1.3 80.0 - - - +
146A ILE* 1.3 60.3 + - - +
148A LYS* 3.9 33.7 + - - +
149A ASP* 5.0 4.8 + - - -
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Residues in contact with ILE 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A LEU* 4.4 7.9 - - + -
94A LEU* 3.8 20.2 - - + +
97A LEU* 3.4 35.7 - - + +
98A ALA* 2.9 43.2 - - - +
101A HIS* 5.0 2.2 - - + +
102A ILE* 5.2 1.6 - - - +
112A PHE* 3.4 37.2 - - + -
142A LEU* 3.0 22.1 + - + +
143A VAL* 2.7 15.9 + - + +
145A ARG* 1.3 71.9 - - - +
147A ALA* 1.3 56.5 + - - +
148A LYS 3.6 1.4 + - - -
149A ASP 5.1 0.7 + - - -
150A LEU* 4.6 4.3 - - - +
160A HEM 4.5 9.0 - - + -
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Residues in contact with ALA 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A LYS* 3.6 31.2 - - + +
112A PHE* 4.1 22.0 - - + -
143A VAL* 2.9 11.8 + - + +
144A ALA* 3.5 4.7 - - - +
146A ILE* 1.3 77.5 - - - +
148A LYS* 1.3 61.0 + - - +
149A ASP 3.3 2.4 + - - -
150A LEU* 3.4 37.7 + - + +
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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
------------------------------------------------------------
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