Contacts of the strand formed by residues 127 - 134 (chain I) in PDB entry 6D6Q
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 ILE 127 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C GLU* 3.8 33.4 - - + +
72I THR* 4.6 12.3 - - + -
73I CYS 3.3 13.7 - - - +
74I LYS* 4.7 17.7 - - + -
88I LEU* 5.9 4.7 - - + -
125I GLY 5.1 3.1 - - - +
126I ASP* 1.3 81.9 - - - +
128I VAL* 1.3 74.6 + - - +
153I VAL* 3.6 1.9 - - - +
154I VAL* 3.3 33.1 + - + +
155I VAL* 3.4 33.0 + - + +
157I HIS* 5.7 7.2 - - + +
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Residues in contact with VAL 128 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72I THR* 3.2 7.3 - - - -
73I CYS* 2.9 56.8 + - - +
75I VAL* 4.3 20.6 - - + -
103I ILE* 4.4 16.8 - - + -
122I PHE* 4.5 13.5 - - + -
126I ASP* 4.0 3.6 + - - +
127I ILE* 1.3 81.9 - - - +
129I LEU* 1.3 67.7 + - - +
130I ALA* 5.2 1.3 - - + -
146I THR* 5.6 0.7 - - + -
152I GLY* 3.0 23.6 - - - +
153I VAL* 3.6 15.7 - - + +
154I VAL* 4.8 1.3 - - - +
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Residues in contact with LEU 129 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70I ILE* 3.7 26.0 - - + -
71I VAL 3.3 13.2 - - - +
72I THR* 3.8 18.6 - - + -
128I VAL* 1.3 76.7 - - - +
130I ALA* 1.3 64.0 + - - +
146I THR* 4.2 0.2 - - - +
150I GLU* 4.9 7.0 - - - +
151I LEU* 3.0 23.9 - - + +
152I GLY* 3.1 27.8 + - - +
154I VAL* 3.5 31.4 - - + -
186I ALA* 4.8 4.0 - - + -
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Residues in contact with ALA 130 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70I ILE* 3.5 8.7 - - - -
71I VAL* 2.9 37.2 + - - +
103I ILE* 4.9 4.5 - - + -
128I VAL* 5.2 1.3 - - + -
129I LEU* 1.3 76.3 - - - +
131I LYS* 1.3 61.7 + - - +
132I VAL 4.1 0.2 - - - -
144I LEU* 3.8 28.0 - - + +
145I THR 3.1 16.2 - - - +
146I THR* 3.6 13.7 - - + -
151I LEU* 3.7 6.0 - - - +
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Residues in contact with LYS 131 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67I VAL* 3.3 20.9 - - + +
68I GLY* 4.2 14.3 - - - -
69I ALA 3.2 22.0 - - - +
70I ILE* 5.3 4.5 - - + -
130I ALA* 1.3 76.4 - - - +
132I VAL* 1.3 66.1 + - - +
133I ILE* 3.1 11.3 - - + +
144I LEU* 4.2 0.9 - - - -
145I THR* 2.9 30.7 + - - +
148I GLU* 5.2 8.8 + - - -
151I LEU* 4.7 2.9 - - + +
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Residues in contact with VAL 132 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65I PRO* 3.9 15.0 - - + +
66I ASP 2.8 35.2 - - - +
67I VAL* 2.6 29.6 - - - +
69I ALA* 4.2 6.2 + - + -
71I VAL* 3.7 25.3 - - + +
87I ILE* 5.4 1.8 - - + -
130I ALA 4.1 0.4 + - - -
131I LYS* 1.3 77.5 - - - +
133I ILE* 1.3 65.3 + - - +
134I SER 5.2 1.1 - - - +
142I TYR* 4.3 20.6 - - + -
143I LEU 3.6 7.2 - - - +
144I LEU* 3.8 20.2 - - + +
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Residues in contact with ILE 133 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67I VAL* 3.4 33.0 - - + +
131I LYS* 3.1 28.7 - - + +
132I VAL* 1.3 77.6 - - - +
134I SER* 1.3 69.0 + - - +
135I LEU 3.9 1.6 + - - -
143I LEU* 3.0 15.3 + - + +
145I THR* 2.8 34.5 - - + +
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Residues in contact with SER 134 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132I VAL* 5.3 1.1 - - - +
133I ILE* 1.3 83.3 + - - +
135I LEU* 1.3 62.3 + - - +
136I GLY* 4.4 5.3 - - - -
141I ASN 4.2 0.5 + - - -
142I TYR* 3.5 5.9 - - - -
143I LEU* 3.2 53.2 + - - +
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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