Contacts of the strand formed by residues 110 - 116 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A LEU* 4.4 20.0 - - + -
87A LEU* 4.0 32.3 - - + -
88A VAL 3.2 11.0 - - - +
89A PRO* 4.1 12.3 - - + -
90A ARG* 4.1 4.0 + - - +
102A TYR* 3.6 6.4 - - - +
103A THR* 2.6 44.1 + - + +
108A PRO* 3.4 28.3 - - + +
109A ARG* 1.4 80.7 - - - +
111A ALA* 1.3 63.5 + - - +
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Residues in contact with ALA 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A GLN 3.4 1.7 - - - +
87A LEU* 3.4 4.6 - - - -
88A VAL 2.5 40.9 + - - +
90A ARG* 4.3 2.7 - - - -
93A LEU* 3.9 21.5 - - + -
100A ARG* 4.9 1.1 - - + -
101A PHE 3.2 5.4 - - - +
102A TYR* 3.6 27.8 - - + -
110A LEU* 1.3 77.5 - - - +
112A LEU* 1.3 61.9 + - - +
113A CYS* 3.6 11.0 + - - -
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Residues in contact with LEU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A PHE* 4.4 14.8 - - + -
14A VAL* 4.4 11.0 - - + -
17A ALA* 5.9 0.4 - - + -
18A CYS* 4.3 18.2 - - - -
23A PHE* 4.1 14.9 - - + -
47A ILE* 4.0 34.8 - - + -
58A LEU* 4.7 2.2 - - + -
85A PHE* 4.1 25.1 - - + -
86A GLN 3.3 18.6 - - - +
87A LEU* 3.8 11.3 - - + +
100A ARG* 3.3 3.6 - - - -
101A PHE* 2.7 54.9 + - + +
111A ALA* 1.3 72.7 - - - +
113A CYS* 1.3 59.3 + - - +
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Residues in contact with CYS 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A PHE* 3.1 11.6 - - - -
86A GLN* 2.8 36.1 + - + +
88A VAL* 4.1 14.8 - - - -
93A LEU* 4.2 7.4 - - - -
94A PRO* 4.4 2.5 - - + -
97A ALA* 3.9 19.1 - - + -
99A LEU 3.1 7.6 - - - +
100A ARG* 4.6 4.9 - - - -
111A ALA* 3.8 24.2 - - - -
112A LEU* 1.3 81.3 - - - +
114A PHE* 1.3 60.4 + - - +
115A VAL* 3.5 20.2 + - + -
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Residues in contact with PHE 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A PHE* 3.9 22.2 - + + -
78A ARG 4.0 17.0 - - - -
79A PHE* 3.9 24.0 - + - -
83A GLY* 4.2 4.0 - - - -
84A SER 3.4 23.8 - - - -
85A PHE* 3.9 24.1 - + + -
97A ALA 3.6 1.0 - - - -
98A HIS* 2.8 30.0 + - + -
99A LEU* 2.8 17.7 + - + +
101A PHE* 5.4 0.8 - - - -
113A CYS* 1.3 72.0 - - - +
115A VAL* 1.3 56.6 + - - +
116A ASP* 3.8 31.6 - - + -
121A GLY* 4.4 4.9 - - - -
122A ARG 4.9 0.2 - - - -
123A TRP* 3.4 37.7 - + - -
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Residues in contact with VAL 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A SER 3.5 2.6 - - - +
83A GLY* 3.2 3.3 - - - -
84A SER* 2.7 49.1 + - - +
86A GLN* 3.7 31.9 - - + +
94A PRO* 4.1 12.6 - - + -
95A ARG 3.8 16.4 - - - +
96A HIS* 3.4 13.0 - - + +
97A ALA* 4.2 4.0 - - - -
113A CYS* 3.7 25.1 - - + +
114A PHE* 1.3 74.8 - - - +
116A ASP* 1.3 65.9 + - - +
117A ILE* 4.9 7.4 - - + +
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Residues in contact with ASP 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A PHE 4.4 0.2 - - - -
82A SER* 2.7 26.5 + - - +
83A GLY* 4.1 9.0 - - - -
96A HIS* 2.9 12.5 + - - -
98A HIS* 3.2 26.6 + - + -
114A PHE* 3.8 20.5 - - + -
115A VAL* 1.3 77.8 - - - +
117A ILE* 1.3 64.9 + - - +
118A ARG 3.3 0.2 + - - -
119A ARG* 3.2 19.2 + - - -
120A PHE 4.0 1.2 + - - -
121A GLY* 2.8 36.0 + - - +
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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