Contacts of the strand formed by residues 136 - 143 (chain C) in PDB entry 1GN6
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A ALA 3.7 26.8 + - - +
3A GLU* 5.1 0.8 - - - +
4A TYR* 3.6 33.6 - - + +
41A ASN* 4.9 4.2 + - - -
44A VAL* 3.5 34.0 - - + +
102C ALA* 6.2 0.7 - - + -
130C TRP* 3.4 7.8 - - - -
131C ASP* 2.7 38.2 + - + +
134C GLY 3.3 15.5 - - - +
135C ASN* 1.3 76.6 - - - +
137C LEU* 1.3 65.6 - - - +
138C LEU* 3.8 17.4 + - + -
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Residues in contact with LEU 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C LEU* 4.9 3.1 - - + -
98C ALA* 4.0 38.4 - - + +
99C ILE* 4.1 18.6 - - + +
102C ALA* 3.9 21.3 - - + +
103C PHE* 3.8 19.7 - - + -
128C LEU* 4.1 9.6 - - + -
129C GLY 3.5 10.1 - - - +
130C TRP* 3.9 18.4 - - + -
136C LYS* 1.3 73.3 - - - +
138C LEU* 1.3 67.4 + - - +
156C LEU* 3.3 34.1 - - + -
194C TYR* 4.5 7.2 - - + -
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Residues in contact with LEU 138 (chain C).
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 7.0 - - - +
44A VAL* 4.7 12.8 - - + -
47A LEU* 5.9 2.5 - - + -
66A LEU* 4.4 15.5 - - + -
70A LEU* 3.7 29.6 - - + -
103C PHE* 4.4 4.0 - - + -
128C LEU* 3.7 4.3 - - - +
129C GLY* 2.9 32.7 + - - +
131C ASP* 3.9 18.8 - - + -
136C LYS* 4.2 19.5 - - + +
137C LEU* 1.3 83.0 - - - +
139C ILE* 1.3 65.8 + - - +
140C PHE* 3.6 25.6 - - + -
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Residues in contact with ILE 139 (chain C).
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* 2.7 31.4 - - - +
66A LEU* 3.6 14.1 - - - +
103C PHE* 3.6 30.6 - - + -
109C PHE* 3.7 22.9 - - + +
112C GLN* 3.8 22.7 + - + +
113C PHE* 3.9 30.7 - - + +
116C ALA* 4.3 14.8 - - + -
126C ALA* 5.2 0.2 - - + -
127C ALA 3.2 12.1 - - - +
128C LEU* 4.1 9.2 - - + -
138C LEU* 1.3 76.6 - - - +
140C PHE* 1.3 65.9 + - - +
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Residues in contact with PHE 140 (chain C).
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* 3.6 4.0 - - - -
66A LEU* 3.9 22.9 - - + -
67A ALA* 4.7 6.5 - - + -
70A LEU* 4.3 2.0 - - + -
151A LEU* 5.8 2.0 - - + -
116C ALA* 4.9 0.2 - - - +
126C ALA* 3.7 2.3 - - - -
127C ALA* 2.7 51.2 + - + +
129C GLY* 4.5 5.4 - - - -
138C LEU* 3.6 43.1 - - + -
139C ILE* 1.3 83.4 - - - +
141C GLN* 1.3 62.0 + - - +
142C VAL* 3.7 4.2 + - + -
148C ASN 4.4 4.5 - - - +
149C PHE* 4.2 18.4 - - + -
150C PRO* 3.5 26.2 - - + -
153C ILE* 3.8 42.6 - - + -
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Residues in contact with GLN 141 (chain C).
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* 4.8 1.0 - - - +
60A LEU* 3.8 29.8 - - - +
63A GLU* 3.8 26.7 + - + +
116C ALA* 2.8 38.9 + - + +
119C THR* 3.0 25.1 + - - -
120C VAL* 3.7 23.3 - - + +
125C TRP 3.8 4.3 - - - +
140C PHE* 1.3 74.5 - - - +
142C VAL* 1.3 59.5 + - - +
143C TYR* 3.9 16.2 + - + -
148C ASN* 2.7 37.8 + - - +
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Residues in contact with VAL 142 (chain C).
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* 4.9 8.3 - - + -
75C ASN* 4.8 1.6 - - - +
120C VAL* 4.3 3.1 - - - +
124C GLY* 3.0 4.9 - - - -
125C TRP* 3.0 46.6 + - + +
127C ALA* 4.1 24.0 - - + -
140C PHE* 4.4 4.5 - - + +
141C GLN* 1.3 74.5 - - - +
143C TYR* 1.3 71.5 + - - +
144C ASP 4.1 5.2 - - - +
145C HIS 3.6 25.6 - - - +
147C THR 3.4 11.9 - - - +
148C ASN 4.7 0.4 - - - -
149C PHE* 3.8 19.1 - - + -
158C LEU* 5.6 0.2 - - + -
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Residues in contact with TYR 143 (chain C).
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 21.3 + - + +
64A LYS* 3.9 26.0 - - + +
120C VAL* 4.6 12.1 - - + -
121C GLN 5.9 1.1 - - - -
123C SER 3.8 5.8 - - - +
141C GLN* 3.9 21.9 + - + -
142C VAL* 1.3 78.5 - - - +
144C ASP* 1.3 74.6 + - - +
145C HIS 3.1 3.6 + - - -
147C THR* 3.0 50.2 + - + -
148C ASN* 3.6 31.8 + - + -
64D LYS* 4.4 15.6 - - - -
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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