Contacts of the strand formed by residues 62 - 74 (chain G) in PDB entry 2Y6T
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 PHE 62 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56G GLN* 3.2 47.1 - - + -
58G ASP 3.6 18.8 - - - -
59G GLU 3.3 17.2 - - - +
60G SER* 3.1 4.7 - - - +
61G ARG* 1.3 94.6 - - + +
63G LYS* 1.3 70.6 + - - +
135G ARG* 5.8 0.2 - - - +
136G TYR* 3.3 29.7 + + + +
156G ILE* 3.9 22.2 - - + -
157G TRP 3.4 14.6 - - - -
158G GLU* 3.4 38.8 - - + -
157H TRP* 3.7 1.1 - - - -
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Residues in contact with LYS 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60G SER 5.4 3.3 + - - -
62G PHE* 1.3 84.4 + - - +
64G VAL* 1.3 64.6 + - - +
133G MET* 3.8 35.4 - - + -
134G GLN 3.6 11.9 - - - +
135G ARG* 4.4 19.8 - - - +
136G TYR* 4.2 4.0 - - - -
156G ILE* 3.5 5.2 - - - +
157G TRP* 2.8 34.8 + - - +
65H GLU* 5.6 4.0 - - - -
133H MET* 4.6 23.3 - - + -
157H TRP* 3.6 22.2 - - + -
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Residues in contact with VAL 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51G ILE* 5.1 1.3 - - + -
53G LEU* 3.8 24.0 - - + -
63G LYS* 1.3 75.1 - - - +
65G GLU* 1.3 62.7 + - - +
66G LEU* 3.9 7.1 + - + -
132G ALA 3.4 2.3 - - - +
133G MET* 3.6 3.5 - - - -
134G GLN* 2.7 43.9 + - + +
135G ARG 4.3 5.8 - - - +
136G TYR* 3.7 23.1 - - + -
142G ILE* 4.3 21.3 - - + -
154G TYR* 4.0 33.2 - - + -
155G ARG 3.8 2.7 - - - +
156G ILE* 4.6 2.9 - - + +
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Residues in contact with GLU 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63G LYS 4.1 0.6 + - - -
64G VAL* 1.3 71.9 - - - +
66G LEU* 1.3 70.4 + - - +
67G LEU* 3.6 19.6 + - + +
132G ALA* 3.4 11.7 - - + +
133G MET* 3.8 13.0 - - - -
154G TYR* 3.3 5.2 - - - +
155G ARG* 2.8 65.0 + - + +
157G TRP* 2.8 43.4 + - + +
63H LYS* 4.3 11.0 + - - +
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Residues in contact with LEU 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51G ILE* 3.8 28.9 - - + -
64G VAL* 3.9 14.6 + - + -
65G GLU* 1.3 74.7 - - - +
67G LEU* 1.3 66.2 + - - +
68G ILE* 3.8 19.3 - - + -
85G LEU* 3.7 15.9 - - + -
98G LEU* 3.4 33.7 - - + -
128G LEU* 3.7 16.7 - - + +
131G ALA 4.7 0.2 - - - +
132G ALA* 2.9 23.7 + - - +
134G GLN* 4.2 10.8 - - + -
142G ILE* 4.6 7.6 - - + -
144G VAL* 4.3 8.1 - - + -
152G VAL* 4.6 4.7 - - + -
153G LYS 3.8 2.7 - - - +
154G TYR* 4.4 3.1 - - + -
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Residues in contact with LEU 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65G GLU* 4.0 32.1 - - - +
66G LEU* 1.3 74.4 - - - +
68G ILE* 1.3 61.1 + - - +
69G GLY 4.1 0.2 + - - -
123G PHE* 4.1 4.5 - - + -
125G THR* 4.4 29.8 - - + +
126G ALA 5.8 0.2 - - - -
128G LEU* 5.1 0.7 - - - -
151G GLU 3.9 2.1 - - - +
153G LYS* 2.8 42.4 + - + +
154G TYR 4.3 4.0 - - - -
155G ARG* 4.1 36.8 - - + +
163H ILE* 3.9 29.2 - - + -
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Residues in contact with ILE 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66G LEU* 3.8 23.6 + - + -
67G LEU* 1.3 76.7 - - - +
69G GLY* 1.3 56.9 + - - +
85G LEU* 3.8 39.5 - - + -
100G MET* 3.9 13.2 - - + -
123G PHE* 4.6 0.2 - - - -
125G THR* 3.5 3.8 - - - -
126G ALA* 2.7 37.1 + - + +
128G LEU* 4.1 20.6 - - + +
144G VAL* 4.6 5.4 - - + -
146G VAL* 3.7 15.9 - - + -
150G VAL* 3.6 20.9 - - + -
151G GLU 3.8 4.7 - - - +
152G VAL* 4.1 17.5 - - + -
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Residues in contact with GLY 69 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68G ILE* 1.3 77.7 - - - +
70G LYS* 1.3 64.4 + - - -
81G LEU* 4.4 6.5 - - - -
103G ILE* 4.7 3.4 - - - -
123G PHE* 3.7 9.8 - - - -
124G VAL 3.1 13.5 - - - -
125G THR* 4.3 0.4 - - - -
126G ALA 4.5 0.2 - - - -
150G VAL* 3.4 8.6 - - - +
151G GLU* 2.9 37.6 + - - +
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Residues in contact with LYS 70 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69G GLY* 1.3 79.2 - - - +
71G THR* 1.3 66.6 + - - +
72G LEU* 3.7 22.6 + - + +
81G LEU* 3.8 19.7 - - + +
103G ILE* 4.1 31.6 - - + +
104G SER 5.5 2.2 + - - -
106G PRO* 6.2 2.4 - - - +
123G PHE* 3.8 5.6 - - - -
124G VAL* 2.8 33.5 + - - +
149G GLY 3.7 20.6 - - - +
150G VAL* 4.1 11.9 - - + -
151G GLU* 4.7 2.0 - - - -
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Residues in contact with THR 71 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70G LYS* 1.3 74.2 - - - +
72G LEU* 1.3 67.7 + - - +
121G VAL* 3.8 21.5 - - + +
122G LYS* 3.3 16.4 - - - +
123G PHE* 3.4 14.8 - - - +
151G GLU* 3.1 23.1 + - - -
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Residues in contact with LEU 72 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70G LYS* 3.7 21.3 + - + +
71G THR* 1.3 80.3 - - - +
73G ASN* 1.3 70.7 + - - +
74G VAL* 3.5 11.5 + - + +
79G HIS* 5.6 8.3 - - + -
81G LEU* 4.7 23.6 - - + -
106G PRO* 5.2 12.1 - - + -
121G VAL* 3.2 8.0 - - - -
122G LYS 2.7 37.7 + - - +
124G VAL* 4.5 16.6 - - + -
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Residues in contact with ASN 73 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72G LEU* 1.3 79.3 - - - +
74G VAL* 1.3 62.0 + - - +
79G HIS* 4.9 3.8 + - - -
119G PRO 6.0 0.3 - - - -
120G GLN 3.8 5.5 - - - +
121G VAL* 3.7 19.7 - - - +
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Residues in contact with VAL 74 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72G LEU* 3.9 15.5 - - + +
73G ASN* 1.3 79.6 - - - +
75G ASP* 1.3 64.1 + - - +
77G ASN 5.3 0.2 - - - +
79G HIS* 3.4 37.9 - - + +
119G PRO* 4.5 4.2 - - - +
120G GLN* 2.8 56.5 + - + +
122G LYS* 3.8 27.8 - - + +
124G VAL* 4.4 8.7 - - + -
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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