Contacts of the strand formed by residues 110 - 116 (chain B) in PDB entry 5ITY
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 LEU 110 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21B LEU* 4.5 15.3 - - + -
23B PHE* 5.5 0.2 - - - -
87B LEU* 4.1 29.6 - - + -
88B VAL* 3.2 18.2 - - - +
89B PRO* 3.7 12.8 - - + -
90B ARG* 4.3 4.6 - - - +
101B PHE 3.7 0.2 - - - +
102B TYR* 3.3 7.3 - - - +
103B THR* 2.7 46.6 + - + +
108B PRO* 3.8 21.5 - - + +
109B ARG* 1.3 85.5 - - - +
111B ALA* 1.3 60.6 + - - +
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Residues in contact with ALA 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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86B GLN 3.5 1.4 - - - +
87B LEU* 3.4 5.5 - - - -
88B VAL* 2.7 44.9 + - + +
90B ARG* 4.2 4.5 - - - +
93B LEU* 3.9 23.3 - - + -
100B ARG* 5.0 1.3 - - + -
101B PHE 3.1 6.1 - - - +
102B TYR* 3.7 24.9 - - + -
110B LEU* 1.3 74.0 - - - +
112B LEU* 1.3 60.4 + - - +
113B CYS* 3.9 6.3 - - - -
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Residues in contact with LEU 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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13B PHE* 4.8 4.0 - - + -
14B VAL* 4.0 24.9 - - + -
17B ALA* 6.2 0.7 - - + -
18B CYS* 4.0 22.0 - - - -
23B PHE* 4.1 8.9 - - + -
47B ILE* 3.9 26.9 - - + -
58B LEU* 4.8 1.3 - - + -
85B PHE* 4.1 23.6 - - + -
86B GLN 3.4 17.5 - - - +
87B LEU* 3.7 16.4 - - + +
100B ARG* 3.4 1.7 - - - -
101B PHE* 2.7 55.0 + - + +
111B ALA* 1.3 71.0 - - - +
113B CYS* 1.3 59.2 + - - +
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Residues in contact with CYS 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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85B PHE* 3.2 11.3 - - - -
86B GLN* 2.6 41.4 + - + +
88B VAL* 3.9 16.4 - - - -
93B LEU* 3.8 28.9 - - - -
94B PRO* 4.5 2.9 - - + -
97B ALA* 4.0 10.8 - - + -
99B LEU 3.2 4.7 - - - +
100B ARG* 3.8 14.6 - - - -
111B ALA* 3.9 3.1 - - - -
112B LEU* 1.3 76.6 - - - +
114B PHE* 1.3 61.1 + - - +
115B VAL* 3.6 18.5 + - + -
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Residues in contact with PHE 114 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35B ASN* 5.5 0.7 - - - -
77B PHE* 3.9 22.4 - + + -
78B ARG 4.3 16.2 - - - -
79B PHE* 3.7 25.8 - + - -
83B GLY* 4.2 4.3 - - - -
84B SER 3.4 20.9 - - - -
85B PHE* 3.8 25.6 - + + -
97B ALA* 3.7 0.9 - - - -
98B HIS* 2.9 29.3 + - + -
99B LEU* 2.7 20.5 + - + +
101B PHE* 5.2 0.4 - - - -
113B CYS* 1.3 71.9 - - - +
115B VAL* 1.3 58.5 + - - +
116B ASP* 3.7 33.2 - - + -
121B GLY* 4.7 4.5 - - - -
122B ARG 4.9 0.2 - - - -
123B TRP* 3.9 32.8 - + - -
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Residues in contact with VAL 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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82B SER 3.7 1.2 - - - +
83B GLY* 3.2 3.3 - - - -
84B SER* 2.9 42.7 + - - +
86B GLN* 3.8 32.8 - - + +
94B PRO* 4.2 12.3 - - + -
95B ARG 3.7 15.0 - - - +
96B HIS* 3.1 14.6 - - + +
97B ALA* 4.3 4.3 - - - -
113B CYS* 4.0 21.8 - - + +
114B PHE* 1.3 76.3 - - - +
116B ASP* 1.3 66.7 + - - +
117B ILE* 5.0 7.6 - - + +
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Residues in contact with ASP 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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79B PHE 4.3 1.1 - - - +
82B SER* 2.8 34.4 + - - +
83B GLY* 4.2 6.3 - - - -
96B HIS* 2.8 12.6 + - - -
98B HIS* 3.2 26.9 + - + -
114B PHE* 3.7 19.9 - - + -
115B VAL* 1.3 76.1 - - - +
117B ILE* 1.3 66.9 + - - +
119B ARG* 3.2 18.0 + - - -
120B PHE 4.2 1.0 + - - -
121B GLY* 2.8 34.9 + - - +
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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