Contacts of the strand formed by residues 61 - 72 (chain B) in PDB entry 1F5J
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 THR 61 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B LEU 3.6 0.2 + - - -
60B GLY* 1.3 73.4 - - - -
62B ILE* 1.3 63.1 + - - +
63B ARG* 3.7 35.6 - - + +
154B THR* 3.9 11.2 - - + -
156B THR* 3.5 11.3 + - - +
157B ASP* 5.3 1.6 - - - +
196B SER 3.5 1.2 - - - +
197B GLN* 3.2 4.9 - - - -
198B SER* 2.7 49.8 + - - +
199B SER 5.2 1.8 - - - -
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Residues in contact with ILE 62 (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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52B TYR* 3.7 40.2 - - + +
59B LEU* 3.9 28.5 - - + +
61B THR* 1.3 75.8 - - - +
63B ARG* 1.3 70.0 + - - +
64B ILE* 4.7 1.1 - - + -
154B THR* 3.6 3.6 - - - -
155B VAL* 3.1 38.5 + - + +
156B THR* 3.2 18.0 + - + +
175B ILE* 4.0 9.4 - - + -
195B PHE* 4.5 13.0 - - + -
196B SER 3.3 5.8 - - - +
197B GLN* 4.0 24.5 - - + +
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Residues in contact with ARG 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B THR* 3.7 22.9 - - + +
62B ILE* 1.3 79.7 - - - +
64B ILE* 1.3 63.3 + - - +
65B THR* 4.1 2.1 + - - +
152B THR* 4.0 19.5 - - + -
153B VAL 3.3 3.6 - - - -
154B THR* 3.7 28.0 + - + +
194B THR 3.6 0.9 - - - +
195B PHE* 3.5 2.6 - - - +
196B SER* 2.8 50.5 + - - +
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Residues in contact with ILE 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ILE* 4.7 1.8 - - + -
63B ARG* 1.3 76.7 - - - +
65B THR* 1.3 67.7 + - - +
66B TYR* 3.8 9.1 + - + -
80B ILE* 3.9 32.8 - - + -
151B GLY 3.6 1.4 - - - +
152B THR* 3.2 2.2 - - - -
153B VAL* 2.8 39.7 + - - +
155B VAL* 4.0 11.0 - - + -
175B ILE* 3.8 19.5 - - + -
176B THR 4.7 3.6 - - - +
177B LEU* 5.2 0.4 - - + -
193B ASN* 3.5 22.7 - - - +
194B THR 3.2 5.6 - - - +
195B PHE* 3.5 41.5 - - + -
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Residues in contact with THR 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ARG* 4.1 1.6 + - - +
64B ILE* 1.3 71.9 - - - +
66B TYR* 1.3 62.2 + - - +
151B GLY* 3.2 9.0 - - - +
152B THR* 2.9 25.3 + - - +
192B GLN* 3.5 28.7 - - - +
194B THR* 2.8 43.9 + - - +
196B SER* 6.1 0.9 - - - -
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Residues in contact with TYR 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ILE* 4.1 15.9 - - + -
65B THR* 1.3 75.4 - - - +
67B SER* 1.3 74.1 + - - +
68B ALA* 5.0 1.6 - - + -
78B LEU* 4.3 13.9 - - + -
80B ILE* 5.2 1.6 - - + -
95B GLU* 2.7 44.6 + - + +
148B ARG* 3.7 8.5 + - - +
149B THR* 3.4 25.8 - - - -
150B SER* 3.2 13.8 + - - -
151B GLY* 2.8 52.3 + - - +
153B VAL* 3.9 13.5 - - + -
177B LEU* 3.5 33.0 - - + -
192B GLN* 3.0 17.1 - - - +
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Residues in contact with SER 67 (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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66B TYR* 1.3 77.5 + - - +
68B ALA* 1.3 65.4 + - - +
149B THR 3.7 7.2 - - - -
150B SER* 3.1 14.9 + - - -
190B ILE* 3.6 2.8 - - - +
191B THR* 2.9 37.1 + - - -
192B GLN* 2.8 36.0 + - - +
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Residues in contact with ALA 68 (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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66B TYR* 5.0 2.9 - - + -
67B SER* 1.3 78.2 - - - +
69B THR* 1.3 66.4 + - - +
70B TYR* 3.7 1.5 + - + -
78B LEU* 4.6 16.8 - - + -
149B THR* 3.0 32.3 + - - +
150B SER* 4.7 0.8 - - - -
189B ASN 3.2 13.2 - - - +
190B ILE* 3.8 23.3 - - + -
191B THR* 4.1 3.3 + - - +
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Residues in contact with THR 69 (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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68B ALA* 1.3 72.6 - - - +
70B TYR* 1.3 59.3 + - - +
71B ASN* 3.2 21.7 - - - +
188B ALA* 3.2 4.9 - - - +
189B ASN* 2.8 48.2 + - - +
191B THR* 5.1 4.7 + - - +
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Residues in contact with TYR 70 (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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38B TRP* 4.7 1.6 - + - -
68B ALA* 3.7 3.5 + - + +
69B THR* 1.3 72.8 - - - +
71B ASN* 1.3 68.9 + - - +
72B PRO* 3.4 33.1 - - + +
76B SER* 2.6 37.1 + - - -
77B TYR* 2.9 30.0 + - - -
78B LEU* 3.8 20.0 - - + -
96B SER* 3.4 33.2 - - - -
97B TRP* 3.6 12.5 - - - -
149B THR* 4.0 19.8 - - + +
179B VAL* 4.2 9.9 - - + -
187B SER 4.3 0.9 - - - -
188B ALA* 4.1 14.8 - - + -
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Residues in contact with ASN 71 (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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69B THR* 3.2 32.3 - - - +
70B TYR* 1.3 77.3 + - - +
72B PRO* 1.3 65.9 - - - +
73B ASN* 4.0 6.3 + - - +
186B GLY* 3.6 3.1 - - - -
187B SER* 2.9 47.2 + - - +
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Residues in contact with PRO 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B TRP* 4.2 4.9 - - + -
70B TYR* 3.4 34.8 - - + +
71B ASN* 1.3 92.5 - - - +
73B ASN* 1.3 61.9 + - - +
74B GLY 3.4 4.7 - - - +
76B SER* 3.5 31.2 - - - +
97B TRP 4.4 1.3 - - - +
98B GLY* 3.9 17.3 - - - -
185B SER 4.2 0.4 - - - +
186B GLY* 4.1 7.6 - - - -
187B SER 4.1 0.2 - - - -
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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