Contacts of the strand formed by residues 124 - 131 (chain H) in PDB entry 1GN2
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 GLY 124 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120H VAL* 3.8 10.7 - - - +
122H GLY 4.0 0.2 + - - -
123H CYS* 1.3 77.0 - - - +
125H TRP* 1.3 63.9 + - - -
142H VAL 3.0 14.6 - - - -
144H ASP 3.6 11.4 - - - -
161H MET* 2.9 30.7 + - - -
162H TRP* 3.4 11.1 - - - +
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Residues in contact with TRP 125 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75H ASN* 3.4 45.4 - - + +
76H HIS* 3.8 21.5 - + - -
79H TRP* 4.0 17.9 - + + -
117H ALA* 5.2 0.2 - - - -
120H VAL* 4.5 6.1 - - - +
124H GLY* 1.3 78.0 - - - -
126H ALA* 1.3 64.9 - - - +
127H ALA* 5.4 1.1 - - + -
141H GLN* 3.7 6.8 - - - +
142H VAL* 3.0 45.1 + - + +
144H ASP 3.2 22.2 + - - -
145H HIS* 3.2 21.6 + - - -
158H LEU* 3.6 31.2 - - + -
159H LEU 3.3 10.1 - - - -
160H ASP* 3.3 47.8 - - + -
161H MET* 4.1 3.4 - - - +
162H TRP* 4.0 3.4 - - - +
999H FE 4.4 0.2 - - - -
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Residues in contact with ALA 126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113H PHE* 3.6 27.5 - - + +
116H ALA* 4.3 5.8 - - + -
117H ALA* 3.4 38.1 - - + +
125H TRP* 1.3 74.3 - - - +
127H ALA* 1.3 62.5 + - - +
139H ILE* 5.5 0.2 - - + -
140H PHE 3.8 4.9 - - - +
141H GLN* 5.0 1.3 - - - +
158H LEU* 3.3 4.2 - - - +
159H LEU 2.9 30.7 + - - +
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Residues in contact with ALA 127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151F LEU* 4.6 9.9 - - + -
113H PHE* 4.0 5.8 - - - -
125H TRP* 5.4 0.9 - - + -
126H ALA* 1.3 75.1 - - - +
128H LEU* 1.3 62.4 + - - +
129H GLY 3.9 0.2 + - - -
138H LEU 3.8 0.2 - - - +
139H ILE* 3.3 3.4 - - - +
140H PHE* 2.8 47.3 + - + +
142H VAL* 4.4 17.3 - - + -
155H PRO* 6.0 0.2 - - + -
157H LEU 3.2 4.7 - - - -
158H LEU* 3.0 28.3 - - + -
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Residues in contact with LEU 128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95H LEU* 5.7 1.3 - - + -
99H ILE* 5.0 7.4 - - + -
103H PHE* 3.9 22.2 - - + -
109H PHE* 3.8 29.6 - - + -
113H PHE* 3.9 12.9 - - + -
127H ALA* 1.3 75.4 - - - +
129H GLY* 1.3 60.3 + - - +
137H LEU* 4.1 16.8 - - + -
138H LEU 3.5 15.0 - - - +
139H ILE* 4.3 3.1 - - + +
155H PRO* 3.9 2.4 - - - +
156H LEU* 2.9 49.8 + - + -
157H LEU* 2.8 25.7 + - + +
158H LEU* 4.9 0.2 - - - +
187H TRP* 5.8 0.7 - - + -
190H VAL* 4.7 9.2 - - + -
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Residues in contact with GLY 129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127H ALA 3.9 1.0 + - - -
128H LEU* 1.3 76.8 - - - +
130H TRP* 1.3 61.3 + - - -
131H ASP 4.0 0.4 + - - -
137H LEU* 3.5 5.7 - - - +
138H LEU* 2.7 36.6 + - - +
140H PHE* 4.6 4.2 - - - -
153H ILE* 4.4 13.5 - - - -
154H VAL 3.0 14.4 - - - -
155H PRO* 4.3 1.1 - - - -
156H LEU* 4.2 6.5 - - - -
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Residues in contact with TRP 130 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129H GLY* 1.3 75.3 - - - -
131H ASP* 1.3 65.5 + - - +
132H THR* 3.6 28.3 + - + +
135H ASN* 3.3 51.4 - - + +
136H LYS* 3.5 20.9 - - - -
137H LEU* 3.7 16.4 - - + -
153H ILE* 3.3 4.2 - - - +
154H VAL* 2.6 38.5 + - + +
156H LEU* 4.3 10.1 - - + -
194H TYR* 4.2 14.1 - + + -
197H ALA* 3.7 38.1 + - + -
198H THR* 3.7 28.3 - - + -
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Residues in contact with ASP 131 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F TYR* 2.8 23.1 + - - -
70F LEU* 4.1 12.3 - - + +
74F VAL* 4.6 5.4 - - - +
129H GLY 4.0 0.2 + - - -
130H TRP* 1.3 73.8 - - - +
132H THR* 1.3 55.0 + - - +
133H LEU* 3.1 18.4 + - - +
134H GLY* 2.6 27.9 + - - -
135H ASN* 2.7 35.7 + - - -
136H LYS* 2.7 19.0 + - - +
138H LEU* 3.8 15.0 - - + +
153H ILE* 3.4 19.7 - - + +
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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
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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