Contacts of the strand formed by residues 136 - 143 (chain B) in PDB entry 1GN3
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 LYS 136 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A ALA* 3.1 29.0 + - - +
3A GLU* 5.1 0.4 - - - +
4A TYR* 3.6 36.2 - - - +
41A ASN* 5.4 1.2 + - - -
44A VAL* 4.0 21.4 - - + +
130B TRP* 3.1 11.4 - - - -
131B ASP* 2.5 33.3 + - + +
134B GLY* 3.0 23.0 - - - +
135B ASN* 1.3 81.5 - - - +
137B LEU* 1.3 59.5 - - - +
138B LEU* 3.8 28.9 - - + -
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Residues in contact with LEU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B LEU* 4.8 4.0 - - + -
98B ALA* 3.9 33.9 - - + -
99B ILE* 4.3 10.5 - - + +
102B ALA* 3.5 24.6 - - + +
103B PHE* 3.3 26.6 - - + -
128B LEU* 4.0 11.9 - - + -
129B GLY 3.6 10.5 - - - +
130B TRP* 4.0 18.8 - - + -
136B LYS* 1.3 71.4 - - - +
138B LEU* 1.3 67.3 + - - +
156B LEU* 3.5 29.4 - - + -
194B TYR* 4.4 8.7 - - + -
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Residues in contact with LEU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A TYR* 4.1 10.8 - - - +
44A VAL* 4.4 7.9 - - + -
47A LEU* 6.0 2.7 - - + -
66A LEU* 4.4 24.7 - - + -
70A LEU* 4.3 7.9 - - + -
103B PHE* 4.1 2.9 - - + -
127B ALA 3.6 0.2 - - - +
128B LEU* 3.1 7.3 - - - +
129B GLY 2.6 42.4 + - - -
131B ASP* 3.8 27.8 - - + +
136B LYS* 3.8 25.8 - - + -
137B LEU* 1.3 80.9 - - - +
139B ILE* 1.3 67.5 + - - +
140B PHE* 4.0 25.8 - - + -
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Residues in contact with ILE 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LEU* 5.0 1.2 - - - +
63A GLU* 2.7 38.0 - - - +
66A LEU* 3.9 12.1 - - - +
103B PHE* 3.4 29.2 - - + -
109B PHE* 3.5 31.0 - - + +
112B GLN* 3.8 25.8 + - + +
113B PHE* 4.2 14.8 - - + -
116B ALA* 3.9 21.1 - - + -
127B ALA 3.1 9.2 - - - +
128B LEU* 4.2 7.0 - - + -
138B LEU* 1.3 81.3 - - - +
140B PHE* 1.3 62.7 - - - +
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Residues in contact with PHE 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A GLU* 3.4 7.4 - - - -
66A LEU* 4.2 19.1 - - + -
67A ALA* 4.6 7.6 - - + -
70A LEU* 4.2 5.8 - - + -
151A LEU* 5.7 2.7 - - + -
116B ALA* 4.9 0.3 - - - +
126B ALA* 3.8 1.6 - - - -
127B ALA* 2.7 40.6 + - + +
129B GLY* 4.3 6.3 - - - -
138B LEU* 4.0 35.9 - - + -
139B ILE* 1.3 83.5 - - - +
141B GLN* 1.3 59.5 + - - +
142B VAL* 3.8 8.7 + - + -
148B ASN 4.4 5.2 - - - +
149B PHE* 3.9 27.8 - - + -
150B PRO* 3.4 19.5 - - + -
153B ILE* 3.7 42.2 - - + -
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Residues in contact with GLN 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ILE* 5.1 0.4 - - - +
60A LEU* 3.8 29.8 - - - +
63A GLU* 3.7 23.8 + - + +
116B ALA* 2.9 24.7 + - - +
119B THR* 2.7 43.4 + - - -
120B VAL* 3.9 15.9 - - + -
125B TRP 3.8 2.9 - - - +
126B ALA* 5.0 1.3 - - - +
140B PHE* 1.3 73.1 - - - +
142B VAL* 1.3 64.4 + - - +
143B TYR* 3.5 25.5 + - + -
148B ASN* 3.1 26.7 + - - +
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Residues in contact with VAL 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A LEU* 4.7 9.0 - - + -
75B ASN* 5.4 1.6 - - - +
120B VAL* 4.4 1.7 - - - +
124B GLY* 2.9 6.8 - - - -
125B TRP* 2.7 55.1 + - + +
127B ALA* 4.1 24.9 - - + -
140B PHE* 4.5 6.7 - - + +
141B GLN* 1.3 74.9 - - - +
143B TYR* 1.3 70.8 + - - +
145B GLN* 4.3 12.6 - - - +
147B THR 3.5 5.4 - - - +
148B ASN* 4.5 0.7 - - - -
149B PHE* 3.2 42.0 - - + -
158B LEU* 5.6 0.2 - - + -
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Residues in contact with TYR 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A LEU* 4.1 13.9 - - + +
64A LYS* 3.8 38.8 - - - +
120B VAL* 4.4 13.2 - - + -
121B GLN 5.5 2.9 - - - -
123B SER 4.1 4.9 - - - +
141B GLN* 3.6 33.4 + - - -
142B VAL* 1.3 75.1 - - - +
144B ASP* 1.3 73.9 + - + +
145B GLN 3.0 4.3 + - - -
146B GLN 3.5 0.2 + - - -
147B THR* 2.8 42.9 + - + +
148B ASN* 3.7 29.7 + - + -
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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