Contacts of the strand formed by residues 113 - 126 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65B LYS* 4.6 4.9 - - - -
66B GLY 3.2 7.2 - - - +
67B GLN* 3.0 27.8 - - - +
68B GLY 4.1 1.1 - - - +
112B LYS* 1.3 93.9 - - + +
114B TRP* 1.3 61.6 + - - +
115B TYR* 4.4 21.9 - - + +
73C HIS* 2.9 37.3 + - + -
75C LEU* 5.7 1.1 - - + -
99C SER* 4.2 0.2 - - - -
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Residues in contact with TRP 114 (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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64B PHE* 3.8 17.7 - - + -
65B LYS* 3.1 10.5 - - - +
66B GLY* 2.8 64.1 + - - -
68B GLY 3.1 26.0 + - - -
69B CYS* 4.5 2.7 - - - -
70B PRO* 4.8 2.1 - - + +
74B VAL* 5.8 0.4 - - + -
76B LEU* 3.8 22.9 - - + -
100B PRO* 3.7 38.4 - - + -
101B CYS* 3.6 17.9 - - - -
112B LYS 4.8 1.8 - - - +
113B PRO* 1.3 75.0 - - - +
115B TYR* 1.3 73.3 + - - +
116B GLU* 4.1 7.4 - - + +
141B TYR* 3.9 29.4 - + - -
73C HIS* 6.0 0.2 - - + -
99C SER* 3.4 11.7 - - - +
102C GLN* 5.6 10.8 - - + +
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Residues in contact with TYR 115 (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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63B LEU* 4.3 5.4 - - + -
64B PHE 3.3 4.3 - - - +
65B LYS* 3.1 36.6 + - + -
113B PRO* 4.4 15.8 - - + +
114B TRP* 1.3 80.6 - - - +
116B GLU* 1.3 76.7 + - - +
143B LEU* 3.3 32.8 - - + -
75C LEU* 3.7 38.2 - - + +
97C ILE* 3.5 50.0 - - + +
98C LYS* 4.0 6.0 - - - +
99C SER* 3.1 20.4 + - - +
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Residues in contact with GLU 116 (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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116A GLU* 4.9 1.6 - - - +
63B LEU* 3.9 1.5 - - - +
64B PHE* 2.9 41.8 + - + +
76B LEU* 4.3 8.5 - - + -
98B LYS* 3.1 52.7 + - + -
99B SER 5.9 0.4 - - - -
100B PRO* 4.4 17.5 - - + +
114B TRP* 4.1 21.7 - - + +
115B TYR* 1.3 83.2 + - - +
117B PRO* 1.3 64.4 - - - +
98C LYS* 3.7 14.6 - - - +
99C SER* 5.0 4.2 + - - +
116C GLU* 4.8 2.4 - - - +
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Residues in contact with PRO 117 (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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117A PRO* 5.6 0.3 - - - +
61B GLN* 4.9 7.2 - - - +
62B VAL 3.4 9.6 - - - +
63B LEU* 4.3 7.2 - - + -
98B LYS* 2.8 31.9 + - - +
116B GLU* 1.3 81.6 - - - +
118B ILE* 1.3 67.9 + - - +
96C ALA* 4.1 24.9 - - + -
97C ILE 3.4 20.4 - - - +
98C LYS* 4.1 23.6 - - + +
117C PRO 5.6 0.2 - - - +
118C ILE* 5.1 7.6 - - + -
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Residues in contact with ILE 118 (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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117A PRO* 5.1 7.4 - - + -
61B GLN* 3.3 9.3 - - - +
62B VAL* 3.1 35.4 + - + -
64B PHE* 3.9 26.7 - - + -
76B LEU 4.3 10.5 - - - +
78B HIS* 3.7 25.7 + - + +
96B ALA* 3.8 29.4 - - + +
97B ILE 4.7 1.6 - - - -
98B LYS* 4.0 31.9 - - + +
117B PRO* 1.3 81.8 - - - +
119B TYR* 1.3 67.1 + - - +
120B LEU* 4.2 1.1 - - + -
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Residues in contact with TYR 119 (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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61A GLN* 3.3 12.0 + - - -
119A TYR* 3.5 55.1 - + + +
59B TYR* 3.5 16.3 - + + +
60B SER 3.6 10.1 - - - -
61B GLN* 4.0 9.6 - - + +
118B ILE* 1.3 77.0 - - - +
120B LEU* 1.3 98.0 + - - +
121B GLY* 4.5 0.9 - - - -
151B TYR* 3.6 20.9 - + - -
57C LEU* 5.7 2.3 - - - +
119C TYR* 3.5 30.7 - + + +
121C GLY* 3.2 38.6 + - - -
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Residues in contact with LEU 120 (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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61A GLN* 3.3 18.4 - - - +
151A TYR* 4.1 3.1 - - - +
59B TYR* 3.1 6.8 - - - +
60B SER 2.9 35.3 + - - +
78B HIS* 3.5 43.7 - - + +
79B THR* 3.8 3.1 - - - -
80B ILE* 4.1 14.1 - - + +
94B LEU* 3.6 33.4 - - + +
95B SER 4.0 5.6 - - - +
96B ALA* 3.7 20.2 - - + -
118B ILE* 4.2 3.1 - - + -
119B TYR* 1.3 94.2 - - - +
121B GLY* 1.3 58.4 + - - +
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Residues in contact with GLY 121 (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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59A TYR* 3.7 1.0 - - - -
119A TYR* 3.3 25.0 + - - -
151A TYR* 3.0 30.3 + - - -
57B LEU* 5.0 2.2 - - - -
58B ILE 3.1 12.6 - - - -
59B TYR* 4.1 4.3 - - - -
94B LEU* 3.7 9.2 - - - +
119B TYR* 4.5 0.9 - - - -
120B LEU* 1.3 76.2 - - - +
122B GLY* 1.3 58.5 + - - -
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Residues in contact with GLY 122 (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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15A HIS* 4.3 3.4 - - - -
59A TYR* 3.5 19.7 - - - -
57B LEU* 3.5 7.2 - - - +
58B ILE 2.9 30.3 + - - +
94B LEU* 3.8 2.6 - - - +
121B GLY* 1.3 73.1 - - - -
123B VAL* 1.3 63.7 + - - -
124B PHE* 3.6 18.2 - - - -
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Residues in contact with VAL 123 (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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13A VAL* 4.1 18.8 - - + -
14A ALA 5.8 0.4 - - - +
15A HIS* 3.8 19.8 + - + +
36A LEU* 4.1 4.6 - - + +
57A LEU* 5.3 0.2 - - + -
59A TYR* 2.9 29.3 + - + +
154A ILE 5.7 0.4 - - - +
155A ILE* 4.1 26.2 - - + -
55B LEU* 4.1 26.0 - - + -
56B TYR 3.2 11.9 - - - +
57B LEU* 4.3 12.6 - - + -
122B GLY* 1.3 74.5 - - - +
124B PHE* 1.3 74.3 + - - +
157B LEU* 4.3 9.0 - - + -
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Residues in contact with PHE 124 (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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15A HIS* 3.6 23.6 - + - -
34A ASN* 3.6 29.8 - - + +
36A LEU* 4.4 3.4 - - - -
54B GLY 3.5 0.9 - - - +
55B LEU* 3.4 7.6 - - - -
56B TYR* 2.8 41.2 + - - +
58B ILE* 4.0 16.4 - - + -
93B LEU* 3.6 51.1 - - + -
94B LEU* 3.6 21.5 - - + -
122B GLY* 3.6 26.2 - - - -
123B VAL* 1.3 77.5 - - - +
125B GLN* 1.3 63.2 + - - +
126B LEU* 3.6 18.8 + - + +
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Residues in contact with GLN 125 (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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6A ARG* 5.0 18.5 - - - +
7A THR 4.2 2.2 + - - -
8A PRO* 3.1 44.8 + - + +
34A ASN* 5.0 2.8 - - - +
36A LEU* 4.2 22.4 - - + +
53B GLU* 5.5 1.9 - - - +
54B GLY* 3.5 14.8 + - - +
55B LEU* 3.4 16.8 - - + +
82B ARG* 3.9 14.0 + - - -
124B PHE* 1.3 71.4 - - - +
126B LEU* 1.3 83.3 + - - +
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Residues in contact with LEU 126 (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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50B VAL* 3.6 29.2 - - + -
52B SER 4.7 0.4 - - - -
53B GLU* 3.3 4.7 - - - +
54B GLY 2.8 31.0 + - - -
56B TYR* 3.8 34.3 - - + -
58B ILE* 4.1 7.4 - - + -
82B ARG* 3.8 22.0 - - - +
93B LEU* 5.0 1.1 - - + -
124B PHE* 3.6 18.8 + - + -
125B GLN* 1.3 92.7 + - - +
127B GLU* 1.3 62.7 + - - +
130B ASP* 3.5 12.6 - - + +
132B LEU* 3.8 20.9 - - + -
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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