Contacts of the strand formed by residues 113 - 126 (chain G) in PDB entry 3IT8
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 PRO 113 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65G LYS* 4.6 5.2 - - - -
66G GLY 3.2 8.1 - - - +
67G GLN* 3.0 27.8 - - - +
68G GLY 4.1 1.1 - - - +
111G ALA 4.7 0.2 - - - +
112G LYS* 1.3 96.6 - - + +
114G TRP* 1.3 61.0 + - - +
115G TYR* 4.4 20.4 - - + +
73I HIS* 2.9 37.0 + - + -
75I LEU* 5.7 0.9 - - + -
99I SER* 4.2 0.3 - - - -
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Residues in contact with TRP 114 (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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64G PHE* 3.8 17.7 - - + -
65G LYS* 3.1 10.6 - - - +
66G GLY* 2.8 66.7 + - - -
68G GLY 3.1 27.7 + - - -
69G CYS* 4.5 2.7 - - - -
70G PRO* 4.9 2.3 - - + +
74G VAL* 5.9 0.7 - - + -
76G LEU* 3.8 22.4 - - + -
100G PRO* 3.7 38.4 - - + -
101G CYS* 3.6 18.1 - - - -
112G LYS 4.8 1.3 - - - -
113G PRO* 1.3 75.1 - - - +
115G TYR* 1.3 73.1 + - - +
116G GLU* 4.1 8.1 - - + +
141G TYR* 3.9 28.9 - + - -
99I SER* 3.3 11.0 - - - +
102I GLN* 5.5 11.9 - - + +
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Residues in contact with TYR 115 (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 LEU* 4.3 4.7 - - + -
64G PHE 3.3 4.7 - - - +
65G LYS* 3.1 36.5 + - + -
113G PRO* 4.4 15.9 - - + +
114G TRP* 1.3 81.6 - - - +
116G GLU* 1.3 76.1 + - - +
143G LEU* 3.3 33.7 - - + -
75I LEU* 3.7 37.8 - - + +
97I ILE* 3.5 51.6 - - + +
98I LYS* 3.9 5.9 - - - +
99I SER* 3.1 20.4 + - - +
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Residues in contact with GLU 116 (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 LEU* 3.9 1.5 - - - +
64G PHE* 2.9 41.1 + - - +
76G LEU* 4.3 9.2 - - + -
98G LYS* 3.1 52.7 + - + -
99G SER 5.8 0.4 - - - -
100G PRO* 4.4 17.7 - - + +
114G TRP* 4.1 21.8 - - + +
115G TYR* 1.3 83.4 - - - +
117G PRO* 1.3 63.4 - - - +
116H GLU* 5.0 1.3 - - - +
98I LYS* 3.6 14.7 - - - +
99I SER* 5.0 4.3 + - - +
116I GLU* 4.8 2.4 - - - +
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Residues in contact with PRO 117 (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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61G GLN* 4.9 7.0 - - - +
62G VAL 3.4 9.9 - - - +
63G LEU* 4.3 7.4 - - + -
98G LYS* 2.9 31.5 + - - +
116G GLU* 1.3 82.2 - - - +
118G ILE* 1.3 69.1 + - - +
96I ALA* 4.1 25.4 - - + -
97I ILE 3.4 20.6 - - - +
98I LYS* 4.1 23.3 - - + +
117I PRO 5.6 0.4 - - - +
118I ILE* 5.1 8.3 - - + -
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Residues in contact with ILE 118 (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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61G GLN* 3.3 8.9 - - - +
62G VAL* 3.1 36.1 + - + -
64G PHE* 3.9 27.1 - - + -
76G LEU 4.3 10.1 - - - +
78G HIS* 3.7 24.9 + - + +
96G ALA* 3.8 29.6 - - + +
97G ILE 4.7 1.8 - - - -
98G LYS* 4.0 32.1 - - + +
117G PRO* 1.3 81.7 - - - +
119G TYR* 1.3 67.2 + - - +
120G LEU* 4.2 1.1 - - + -
117H PRO* 5.1 6.3 - - + -
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Residues in contact with TYR 119 (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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59G TYR* 3.5 16.8 - + + +
60G SER 3.5 10.3 - - - -
61G GLN* 4.0 10.3 - - + +
118G ILE* 1.3 76.1 - - - +
120G LEU* 1.3 96.1 + - - +
121G GLY* 4.3 1.1 - - - -
151G TYR* 3.6 20.6 - + - -
61H GLN* 3.3 10.7 + - - -
119H TYR* 3.5 36.0 - + + +
57I LEU* 5.7 2.3 - - - +
119I TYR* 3.5 52.4 - + + +
121I GLY* 3.2 39.0 + - - -
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Residues in contact with LEU 120 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59G TYR* 3.1 6.4 - - - +
60G SER 2.9 35.2 + - - +
78G HIS* 3.5 43.7 - - + +
79G THR* 3.8 3.8 - - - -
80G ILE* 4.1 13.9 - - + +
94G LEU* 3.7 34.3 - - + +
95G SER 4.0 4.5 - - - +
96G ALA* 3.7 19.5 - - + -
118G ILE* 4.2 2.9 - - + -
119G TYR* 1.3 92.9 - - - +
121G GLY* 1.3 58.0 + - - +
61H GLN* 3.2 19.5 - - - +
119H TYR* 4.8 0.2 - - - -
151H TYR* 4.1 2.2 - - - +
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Residues in contact with GLY 121 (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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57G LEU* 5.0 2.0 - - - -
58G ILE 3.1 11.9 - - - -
59G TYR* 4.1 4.7 - - - -
94G LEU* 3.6 8.7 - - - +
119G TYR* 4.4 0.7 - - - -
120G LEU* 1.3 76.8 - - - +
122G GLY* 1.3 58.3 + - - -
59H TYR* 3.7 1.0 - - - -
119H TYR* 3.2 26.4 + - - -
151H TYR* 3.0 29.3 + - - -
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Residues in contact with GLY 122 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57G LEU* 3.6 6.4 - - - +
58G ILE 2.9 30.5 + - - +
94G LEU* 3.7 5.4 - - - +
121G GLY* 1.3 74.6 - - - -
123G VAL* 1.3 63.2 + - - -
124G PHE* 3.5 19.9 - - - -
15H HIS* 4.3 0.4 - - - -
59H TYR* 3.5 18.4 - - - -
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Residues in contact with VAL 123 (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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55G LEU* 4.1 18.4 - - + -
56G TYR 3.2 12.8 - - - +
57G LEU* 4.3 12.8 - - + -
122G GLY* 1.3 74.5 - - - +
124G PHE* 1.3 76.1 + - - +
157G LEU* 4.3 8.7 - - + -
13H VAL* 4.1 25.8 - - + -
14H ALA 5.7 0.2 - - - +
15H HIS* 3.7 19.6 - - + +
36H LEU* 4.1 3.9 - - + +
57H LEU* 5.3 0.4 - - + -
59H TYR* 2.8 30.4 + - + +
155H ILE* 4.0 26.5 - - + -
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Residues in contact with PHE 124 (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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54G GLY 3.5 0.9 - - - +
55G LEU* 3.4 7.3 - - - -
56G TYR* 2.8 42.0 + - - +
58G ILE* 4.0 16.2 - - + -
93G LEU* 3.7 42.2 - - + -
94G LEU* 3.6 27.1 - - + -
122G GLY* 3.5 29.8 - - - -
123G VAL* 1.3 75.1 - - - +
125G GLN* 1.3 61.5 + - - +
126G LEU* 3.6 18.8 + - + -
15H HIS* 3.6 23.6 - + - -
34H ASN* 3.6 30.3 - - + -
36H LEU* 4.3 3.6 - - - -
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Residues in contact with GLN 125 (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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53G GLU* 5.5 1.7 - - - +
54G GLY* 3.5 14.9 + - - +
55G LEU* 3.4 17.9 - - + +
82G ARG* 3.9 14.4 + - - -
124G PHE* 1.3 70.9 - - - +
126G LEU* 1.3 82.9 + - - +
6H ARG* 5.1 17.6 - - - +
7H THR 4.2 1.6 + - - -
8H PRO* 3.0 45.8 + - + +
34H ASN* 5.0 2.4 - - - +
36H LEU* 4.0 22.4 - - + +
160K TYR* 5.2 1.3 + - - -
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Residues in contact with LEU 126 (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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50G VAL* 3.6 30.5 - - + -
52G SER 4.0 0.6 - - - +
53G GLU* 3.3 5.8 - - - +
54G GLY 2.8 33.2 + - - -
56G TYR* 3.8 37.0 - - + -
58G ILE* 4.0 7.2 - - + -
82G ARG* 3.9 20.0 - - - +
93G LEU* 5.0 1.3 - - + -
124G PHE* 3.6 19.0 + - + -
125G GLN* 1.3 93.3 + - - +
127G GLU* 1.3 61.3 + - - +
130G ASP* 3.5 13.2 - - + +
132G LEU* 3.9 19.7 - - + -
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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