Contacts of the strand formed by residues 109 - 114 (chain B) in PDB entry 3FWQ
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 109 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33B TRP* 3.6 29.2 - - + -
69B ILE* 4.1 0.3 - - - -
70B LEU* 3.1 48.2 + - + +
71B LYS 5.6 2.0 - - - +
78B ILE* 3.6 33.4 - - + -
100B ILE* 5.4 1.8 - - + -
101B VAL 3.5 7.6 - - - +
102B LYS* 4.2 5.4 - - + -
107B ARG 4.2 3.1 - - - +
108B THR* 1.3 94.1 + - - +
110B ALA* 1.3 58.9 + - - +
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Residues in contact with ALA 110 (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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33B TRP* 5.1 0.2 - - - -
67B VAL* 4.0 11.9 - - + -
68B LYS 3.3 5.6 - - - +
69B ILE* 3.8 29.8 - - + -
100B ILE* 4.9 1.1 - - - -
101B VAL* 2.8 46.9 + - + +
103B ASP* 4.7 6.7 - - - +
108B THR 3.5 5.1 + - - +
109B PRO* 1.3 74.1 - - - +
111B LEU* 1.3 64.9 - - - +
112B VAL* 3.6 0.3 + - - +
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Residues in contact with LEU 111 (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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66B VAL 3.5 1.4 - - - +
67B VAL* 3.3 4.3 - - - -
68B LYS* 2.7 45.2 + - + +
70B LEU* 3.7 31.9 - - + -
81B GLU* 3.2 29.2 - - - +
82B ILE* 4.2 23.8 - - + -
85B LEU* 3.8 8.5 - - + -
97B LEU* 4.0 14.6 - - + -
99B ASP 4.4 1.3 - - - -
100B ILE* 4.5 7.6 - - + -
110B ALA* 1.3 71.0 - - - +
112B VAL* 1.3 61.1 + - - +
113B PHE* 3.5 36.1 + - + -
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Residues in contact with VAL 112 (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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39B TYR* 3.9 40.2 - - + -
65B VAL* 4.3 11.0 - - + -
66B VAL 3.5 6.7 - - - +
67B VAL* 4.5 9.2 - - + +
97B LEU* 3.4 4.3 - - - +
98B ALA* 2.7 37.8 + - + -
99B ASP* 3.0 29.8 + - + +
101B VAL* 3.8 28.5 - - + -
110B ALA 3.8 0.9 - - - +
111B LEU* 1.3 74.4 - - - +
113B PHE* 1.3 62.7 + - - +
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Residues in contact with PHE 113 (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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65B VAL* 3.4 12.5 - - - +
66B VAL* 2.8 41.3 + - + +
68B LYS* 3.6 36.1 - - + -
85B LEU* 3.7 24.2 - - + -
95B ILE* 3.4 45.1 - - + -
96B THR 3.4 9.6 - - - -
97B LEU* 4.0 13.2 - - + -
98B ALA* 4.2 4.5 - - - +
111B LEU* 3.5 37.2 - - + -
112B VAL* 1.3 74.0 - - - +
114B GLU* 1.3 64.9 + - - +
175B ASP 5.9 2.2 - - - -
176B TRP* 6.1 0.9 - + - -
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Residues in contact with GLU 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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89A ARG* 4.2 27.7 + - - +
63B GLU* 4.3 12.5 - - - +
64B LYS 4.6 0.5 - - - +
65B VAL* 4.9 4.5 - - - -
66B VAL* 3.9 4.5 - - - +
95B ILE* 3.3 20.8 - - + +
96B THR* 2.9 30.2 + - + +
98B ALA* 4.5 5.4 - - + +
113B PHE* 1.3 77.6 - - - +
115B HIS* 1.3 101.3 + - - +
116B VAL* 3.5 2.9 + - - +
170B LYS* 4.6 7.7 + - - -
172B ARG* 5.0 7.1 + - - -
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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