Contacts of the strand formed by residues 81 - 90 (chain B) in PDB entry 3L3T
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 GLN 81 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A LEU* 3.5 28.6 - - + +
78A GLY* 4.4 15.6 + - - +
65B VAL 3.5 0.3 - - - +
66B ARG* 3.6 0.9 - - - -
67B LEU* 3.0 47.1 + - + +
79B ASN 4.2 5.5 + - - +
80B GLU* 1.3 77.3 - - - +
82B PHE* 1.3 63.1 + - - +
83B ILE* 4.5 0.7 - - + -
112B ALA* 3.6 7.8 - - - +
113B VAL* 2.9 53.9 + - - +
115B ASN* 3.8 11.1 - - - +
118B VAL* 3.6 20.7 - - + +
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Residues in contact with PHE 82 (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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64A GLN* 5.8 0.4 - - - -
76A LEU* 4.6 5.7 - - - +
82A PHE* 3.7 65.8 - + + -
64B GLN* 3.8 26.9 - - - +
65B VAL 3.6 3.6 - - - -
66B ARG* 3.6 48.2 - - + -
70B GLU* 4.3 4.3 - - - -
76B LEU* 4.2 11.7 - - + -
80B GLU* 3.6 32.5 - - + -
81B GLN* 1.3 73.9 - - - +
83B ILE* 1.3 66.7 + - - +
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Residues in contact with ILE 83 (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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76A LEU* 3.4 32.8 - - + -
64B GLN* 4.3 2.1 - - - +
65B VAL* 2.8 38.7 + - - +
67B LEU* 4.0 21.5 - - + -
81B GLN* 4.2 4.3 - - - +
82B PHE* 1.3 80.1 - - - +
84B ASN* 1.3 75.3 + - - +
108B LEU* 3.9 14.0 - - + +
109B SER* 3.8 2.2 - - - +
110B SER* 3.6 45.8 - - - +
112B ALA* 4.0 14.8 - - - +
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Residues in contact with ASN 84 (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 ILE 3.8 4.5 - - - +
64B GLN* 3.4 31.6 + - - +
65B VAL* 5.4 0.4 - - - -
83B ILE* 1.3 78.6 - - - +
85B ALA* 1.3 64.3 + - - +
108B LEU* 3.9 1.3 - - - -
109B SER* 2.7 37.7 + - - +
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Residues in contact with ALA 85 (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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62B ARG* 3.7 19.1 + - - -
63B ILE* 2.9 25.9 + - + +
65B VAL* 4.9 2.2 - - + -
83B ILE 3.7 0.6 + - - -
84B ASN* 1.3 75.8 - - - +
86B ALA* 1.3 60.5 + - - +
87B LYS 4.4 0.2 - - - +
88B ILE* 4.0 23.3 - - + -
106B ILE* 3.4 28.7 - - + -
107B LYS 3.5 6.1 - - - +
108B LEU* 4.6 0.7 - - - +
109B SER* 4.7 1.3 - - - -
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Residues in contact with ALA 86 (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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62B ARG* 3.5 19.6 + - - +
84B ASN 3.6 3.0 + - - -
85B ALA* 1.3 73.4 - - - +
87B LYS* 1.3 72.5 + - + +
107B LYS* 2.8 20.2 + - + +
108B LEU 4.2 3.1 - - - +
109B SER* 3.8 25.8 - - - +
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Residues in contact with LYS 87 (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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62B ARG* 5.0 2.5 - - - +
86B ALA* 1.3 86.8 + - - +
88B ILE* 1.3 66.1 + - - +
89B ILE* 4.2 16.1 - - + +
105B LEU 3.9 0.2 - - - +
106B ILE* 3.4 5.5 - - - +
107B LYS* 2.8 74.3 + - + +
245B ASN* 3.1 35.4 - - - +
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Residues in contact with ILE 88 (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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59B TYR* 3.5 28.6 + - + +
60B LYS 3.0 26.7 - - - +
61B THR* 3.3 19.3 - - - +
62B ARG* 4.2 8.8 - - - +
63B ILE* 4.0 22.9 - - + +
85B ALA* 4.0 15.3 - - + -
87B LYS* 1.3 79.7 - - - +
89B ILE* 1.3 61.6 + - - +
90B ARG 4.1 0.4 + - - -
104B MET* 3.5 33.7 - - + -
105B LEU 3.6 2.2 - - - -
106B ILE* 4.3 9.4 - - + -
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Residues in contact with ILE 89 (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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51B TRP* 4.3 18.4 - - + -
87B LYS* 4.6 11.7 - - + -
88B ILE* 1.3 83.1 - - - +
90B ARG* 1.3 72.5 + - - +
91B HIS 3.7 0.2 + - - -
92B PRO* 5.9 0.7 - - + -
104B MET* 3.5 4.2 - - - -
105B LEU* 2.9 37.0 + - + +
237B TRP* 3.9 16.0 - - + +
241B THR* 3.7 26.9 - - + -
245B ASN* 4.3 15.5 - - - +
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Residues in contact with ARG 90 (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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56B ALA* 3.6 32.5 - - + +
59B TYR* 3.4 64.2 + - + +
88B ILE 4.1 2.2 + - - -
89B ILE* 1.3 84.7 - - - +
91B HIS* 1.3 70.9 + - - +
92B PRO* 3.2 4.5 - - - +
94B TYR* 4.5 13.4 - - + -
96B ARG* 4.8 12.7 - - - +
103B ILE 4.0 3.8 - - - -
104B MET* 4.2 3.8 - - - -
237B TRP* 4.3 0.4 - - - -
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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