Contacts of the strand formed by residues 153 - 160 (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 ILE 153 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74F VAL* 6.3 0.2 - - + -
151F LEU* 4.0 23.1 - - + +
152F GLY* 3.2 26.0 + - - +
129H GLY* 4.4 5.2 - - - -
130H TRP 3.3 19.3 - - - +
131H ASP* 3.4 25.6 - - + +
140H PHE* 3.6 31.9 - - + -
149H PHE* 5.5 0.9 - - + -
150H PRO* 3.8 40.7 + - + +
151H LEU 3.3 3.1 - - - +
152H GLY* 1.3 77.5 - - - +
154H VAL* 1.3 69.0 + - - +
155H PRO* 3.4 0.7 - - + +
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Residues in contact with VAL 154 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152F GLY* 4.9 2.7 - - - -
129H GLY* 3.0 5.5 - - - -
130H TRP* 2.6 58.5 + - + +
132H THR* 4.1 12.3 - - + -
152H GLY 4.4 3.1 - - - +
153H ILE* 1.3 73.3 - - - +
155H PRO* 1.3 76.7 - - + +
156H LEU* 3.6 4.8 + - + +
193H ARG* 5.3 1.8 - - + +
197H ALA* 4.2 24.9 - - + +
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Residues in contact with PRO 155 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151F LEU* 4.0 39.3 - - + +
152F GLY* 3.9 12.1 - - - +
74H VAL* 5.4 0.7 - - + -
78H ILE* 3.7 27.8 - - + +
127H ALA* 6.1 0.2 - - + -
128H LEU 3.9 5.4 - - - +
129H GLY* 4.3 1.1 - - - -
153H ILE* 3.4 9.3 - - - +
154H VAL* 1.3 94.7 - - + +
156H LEU* 1.3 67.5 + - - +
158H LEU* 4.6 8.3 - - + -
193H ARG* 4.0 14.7 + - - +
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Residues in contact with LEU 156 (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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78H ILE* 4.6 2.8 - - - +
82H ASN* 3.4 11.0 + - - -
95H LEU* 5.5 1.1 - - + -
128H LEU* 2.9 32.6 + - + +
129H GLY 4.3 4.0 - - - -
130H TRP* 4.3 2.9 - - + -
137H LEU* 3.6 31.9 - - + -
154H VAL* 3.9 13.0 - - + +
155H PRO* 1.3 82.0 - - - +
157H LEU* 1.3 60.1 + - - +
190H VAL* 4.1 14.6 - - + +
193H ARG* 3.3 55.3 - - + +
194H TYR* 3.8 19.1 - - + +
197H ALA* 4.2 10.3 - - + -
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Residues in contact with LEU 157 (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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82H ASN* 3.3 27.1 - - + +
109H PHE* 4.4 10.5 - - + -
113H PHE* 4.2 17.2 - - + -
126H ALA 3.9 0.2 - - - +
127H ALA* 3.2 0.9 - - - -
128H LEU* 2.8 41.3 + - + -
156H LEU* 1.3 79.9 - - - +
158H LEU* 1.3 69.2 + - - +
181H PHE* 3.9 23.3 - - + -
182H TRP* 4.4 13.5 - - + -
185H VAL* 4.1 8.5 - - + -
187H TRP* 4.2 27.4 - - + -
190H VAL* 4.0 19.1 - - + -
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Residues in contact with LEU 158 (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* 4.2 13.7 - - + -
74H VAL* 6.2 0.2 - - + -
75H ASN* 3.9 42.8 - - - +
78H ILE* 4.3 20.0 - - + -
79H TRP* 3.5 18.1 - - + -
82H ASN* 2.9 13.3 + - - +
113H PHE* 4.5 2.7 - - - -
125H TRP* 3.6 24.5 - - + -
126H ALA 3.3 4.3 - - - +
127H ALA* 3.0 33.7 - - + -
128H LEU 4.5 0.7 - - - +
155H PRO* 4.6 8.3 - - + -
157H LEU* 1.3 83.9 - - - +
159H LEU* 1.3 62.7 - - - +
160H ASP 4.1 0.7 - - - -
181H PHE* 3.8 10.0 - - - -
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Residues in contact with LEU 159 (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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79H TRP* 3.8 3.6 - - + -
113H PHE* 3.8 26.2 - - + -
114H HIS* 6.1 1.3 - - + -
117H ALA* 4.1 15.0 - - + -
125H TRP* 3.3 3.9 - - - -
126H ALA* 2.9 29.2 + - + +
158H LEU* 1.3 74.2 - - - +
160H ASP* 1.3 68.8 + - - +
161H MET* 3.3 12.6 + - - +
177H PHE* 3.5 36.3 - - + -
178H ALA* 4.2 19.3 - - + +
181H PHE* 3.7 38.8 - - + -
182H TRP* 5.7 0.4 - - - +
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Residues in contact with ASP 160 (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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28H HIS* 2.9 14.6 + - - -
76H HIS* 3.6 1.2 + - - -
79H TRP* 3.6 17.4 - - + -
125H TRP* 3.3 31.9 - - + -
159H LEU* 1.3 70.0 - - - +
161H MET* 1.3 58.5 + - - +
162H TRP* 2.8 41.2 + - - +
164H HIS* 3.4 0.5 + - - -
165H ALA* 3.5 17.4 - - + +
177H PHE* 3.4 23.9 - - - -
999H FE 2.0 30.7 - - - -
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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