Contacts of the helix formed by residues 155 - 169 (chain A) in PDB entry 1GAJ
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 SER 155 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A LEU* 1.3 77.0 - - - +
156A GLY* 1.3 59.2 + - - +
157A GLY 3.4 2.7 + - - -
158A GLN* 2.9 42.9 + - - +
159A MET* 2.8 28.0 + - - +
188A LEU* 3.7 11.3 - - - +
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Residues in contact with GLY 156 (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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155A SER* 1.3 73.7 - - - +
157A GLY* 1.3 56.6 + - - +
159A MET* 3.4 7.6 + - - +
160A LYS* 3.0 33.8 + - - +
183A GLY 5.1 7.0 - - - -
184A VAL* 3.9 9.2 - - - -
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Residues in contact with GLY 157 (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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155A SER* 3.3 3.6 + - - -
156A GLY* 1.3 72.8 - - - +
158A GLN* 1.3 65.4 + - - +
160A LYS* 3.3 3.3 + - - +
161A LEU* 3.0 20.6 + - - +
184A VAL* 3.5 33.9 - - - +
188A LEU* 3.7 17.7 - - - +
192A ILE* 3.5 9.1 - - - +
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Residues in contact with GLN 158 (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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143A LEU* 5.0 7.8 - - + +
145A HIS* 5.6 1.4 + - - -
146A LEU* 3.9 29.6 - - + +
154A LEU* 3.6 21.8 - - + +
155A SER* 2.9 47.6 + - - +
157A GLY* 1.3 77.7 - - - +
159A MET* 1.3 57.6 + - - +
161A LEU* 2.8 25.3 + - - +
162A VAL* 3.0 17.8 + - + +
188A LEU* 4.2 12.4 - - + +
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Residues in contact with MET 159 (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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90A THR* 3.6 30.7 - - + +
95A LYS* 4.5 13.9 - - - +
102A ASN* 4.5 2.7 - - - +
151A ALA* 3.8 37.9 - - + +
154A LEU* 4.2 7.3 - - + +
155A SER 2.8 16.1 + - - +
156A GLY* 3.6 8.3 - - - +
158A GLN* 1.3 77.2 - - - +
160A LYS* 1.3 62.7 + - + +
162A VAL* 3.1 33.9 + - + -
163A GLU* 3.1 36.1 + - + +
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Residues in contact with LYS 160 (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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89A GLN* 4.8 14.5 - - - +
156A GLY 3.0 24.2 + - - +
157A GLY 3.4 8.3 - - - +
158A GLN 3.2 0.2 - - - -
159A MET* 1.3 76.5 - - + +
161A LEU* 1.3 62.6 + - - +
163A GLU* 3.3 25.7 + - - +
164A ILE* 3.2 27.1 + - + +
178A ASP 5.2 1.4 + - - -
179A GLN 3.6 17.0 + - - -
180A PRO* 3.2 29.1 - - + +
182A ALA* 4.4 15.0 - - - +
184A VAL* 3.8 10.3 - - + -
192A ILE* 3.7 9.2 - - + -
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Residues in contact with LEU 161 (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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141A LEU* 3.4 39.2 - - + +
143A LEU* 3.8 27.8 - - + -
157A GLY 3.0 11.3 + - - +
158A GLN* 2.8 12.4 + - - +
160A LYS* 1.3 78.0 - - - +
162A VAL* 1.3 63.0 + - - +
164A ILE* 3.2 25.0 + - + +
165A GLY 3.0 17.0 + - - -
188A LEU* 5.8 5.4 - - + -
191A ASP* 5.5 2.9 - - - +
192A ILE* 4.2 18.1 - - + +
195A HIS* 4.0 28.5 - - + +
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Residues in contact with VAL 162 (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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99A VAL* 4.0 20.9 - - + -
102A ASN* 3.9 17.0 - - + -
103A LEU* 3.6 21.9 - - + +
138A LEU* 6.1 0.2 - - - -
141A LEU* 5.1 0.2 - - - -
143A LEU* 4.4 14.4 - - + -
154A LEU* 3.7 25.1 - - + -
158A GLN 3.0 14.4 + - - +
159A MET* 3.4 23.6 - - + +
161A LEU* 1.3 74.9 - - - +
163A GLU* 1.3 55.3 + - - +
165A GLY* 2.9 4.4 + - - +
166A ARG* 2.8 32.7 + - - +
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Residues in contact with GLU 163 (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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87A THR* 4.1 15.8 - - - +
88A PHE 3.2 28.0 + - - +
89A GLN* 3.8 6.8 - - - +
90A THR* 2.7 35.8 + - - +
159A MET* 3.1 24.1 + - + +
160A LYS* 3.5 34.9 + - - +
161A LEU 3.2 0.2 - - - -
162A VAL* 1.3 71.8 - - - +
164A ILE* 1.3 67.6 + - + +
166A ARG* 3.1 25.9 + - - +
167A ALA* 3.1 13.5 + - - +
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Residues in contact with ILE 164 (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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87A THR* 4.1 11.4 - - + -
141A LEU* 5.0 6.3 - - + -
160A LYS* 3.2 14.1 + - + +
161A LEU* 3.2 19.4 + - + +
163A GLU* 1.3 75.7 - - + +
165A GLY* 1.3 62.6 + - - +
167A ALA* 3.0 5.7 + - - +
168A LEU* 3.0 37.4 + - + +
175A ILE* 4.8 9.9 - - + -
177A MET* 4.2 26.9 - - + -
180A PRO* 5.4 3.1 - - + -
192A ILE* 3.8 29.6 - - + +
195A HIS* 6.0 2.2 - - + -
196A VAL* 5.2 7.0 - - + -
199A LEU* 4.7 11.7 - - + -
206A PHE* 5.7 1.8 - - + -
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Residues in contact with GLY 165 (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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103A LEU* 3.8 13.7 - - - +
137A ILE* 3.8 12.4 - - - +
141A LEU* 3.7 21.3 - - - +
161A LEU 3.0 7.5 + - - -
162A VAL 2.9 8.5 + - - -
164A ILE* 1.3 77.8 - - - +
166A ARG* 1.3 61.0 + - - +
168A LEU* 3.3 12.6 + - - +
169A MET* 3.4 14.9 + - - +
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Residues in contact with ARG 166 (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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88A PHE* 2.9 44.5 + - - +
90A THR* 2.9 27.7 + - - +
94A LEU* 3.9 8.4 - - - +
102A ASN* 2.9 50.5 + - - +
103A LEU* 3.8 10.7 - - - +
105A ILE* 4.0 15.9 - - - +
106A GLY* 4.3 14.9 - - - +
114A PRO* 4.7 11.1 - - - +
159A MET* 4.7 1.6 - - - +
162A VAL* 2.8 12.0 + - - +
163A GLU* 3.1 26.3 + - - +
165A GLY* 1.3 74.8 - - - +
167A ALA* 1.3 61.9 + - - +
169A MET* 3.2 24.8 - - - +
170A THR* 4.4 3.5 + - - +
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Residues in contact with ALA 167 (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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85A VAL* 3.5 29.2 - - + -
86A ARG 4.5 5.6 - - - +
87A THR* 4.0 19.1 - - + -
163A GLU 3.1 9.8 + - - +
164A ILE* 3.0 9.9 + - - +
166A ARG* 1.3 72.7 - - - +
168A LEU* 1.3 61.1 + - - +
169A MET 2.9 5.5 + - - -
170A THR* 2.7 28.0 + - - -
172A PRO* 3.3 5.7 - - - +
175A ILE* 4.6 7.4 - - + -
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Residues in contact with LEU 168 (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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133A LYS* 5.1 0.3 - - - +
137A ILE* 3.8 33.5 - - + +
140A PHE* 4.9 4.9 - - + -
141A LEU* 4.5 9.6 - - + -
164A ILE* 3.0 31.6 + - + +
165A GLY* 3.3 8.7 + - - +
167A ALA* 1.3 70.0 - - - +
169A MET* 1.3 56.7 + - - +
170A THR 2.9 6.1 - - - -
171A ASN* 2.9 25.9 + - - +
172A PRO* 3.7 7.0 - - + -
175A ILE* 4.3 11.2 - - + -
199A LEU* 3.9 36.6 - - + -
204A ILE* 4.0 17.0 - - + -
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Residues in contact with MET 169 (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 TYR* 5.7 0.2 + - - -
103A LEU* 3.2 40.2 - - + +
104A LEU* 3.9 15.7 - - + +
106A GLY* 4.8 4.0 - - - -
107A GLU* 3.2 38.9 - - + +
130A MET 4.1 5.4 - - - +
133A LYS* 3.1 32.9 + - - +
134A ALA* 3.7 22.9 - - + -
137A ILE* 3.7 20.0 - - + -
165A GLY 3.4 15.6 + - - +
166A ARG 3.2 12.8 - - - +
167A ALA 2.9 0.8 + - - -
168A LEU* 1.3 77.4 - - - +
170A THR* 1.3 60.9 + - + +
171A ASN* 3.4 2.9 + - - -
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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