Contacts of the strand formed by residues 113 - 122 (chain A) in PDB entry 6IY6
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 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A ARG* 3.7 26.5 - - + -
64A ALA* 3.4 13.5 - - - +
65A ARG* 3.8 23.1 - - + +
112A SER* 1.3 71.2 - - - +
114A VAL* 1.3 65.7 + - - +
144A VAL* 3.6 1.2 - - - -
145A ILE* 3.2 36.6 + - + -
146A SER* 2.9 14.3 + - - +
462B GLY* 3.5 26.9 - - - +
463B ALA 3.6 2.2 - - - +
464B PRO* 3.4 43.3 - - + -
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Residues in contact with VAL 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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62A VAL 3.5 2.4 - - - +
63A ARG* 3.3 4.0 - - - -
64A ALA 2.8 43.5 + - - +
66A VAL* 4.0 30.1 - - + -
78A LEU* 6.0 0.9 - - + -
80A LEU* 4.0 11.0 - - + -
108A ILE* 4.1 12.1 - - + -
112A SER 4.3 1.8 - - - +
113A ILE* 1.3 76.9 - - - +
115A ASP* 1.3 61.9 + - - +
116A VAL* 3.8 21.3 - - + +
142A ILE* 4.3 4.9 - - + -
143A TYR 3.1 9.0 - - - +
144A VAL* 3.8 26.2 - - + -
145A ILE 4.5 0.4 - - - +
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Residues in contact with ASP 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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43A ARG* 4.3 3.0 + - - +
45A LEU* 5.1 1.6 - - + -
61A TRP* 4.0 19.0 - - + -
62A VAL 3.5 4.9 - - - -
63A ARG* 2.7 42.3 + - - +
114A VAL* 1.3 70.5 - - - +
116A VAL* 1.3 58.1 + - - +
141A LYS 4.2 0.2 - - - +
142A ILE* 3.5 2.9 - - - -
143A TYR* 2.8 45.2 + - + +
145A ILE* 3.4 19.8 - - + +
297B TYR* 2.6 30.1 + - - -
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Residues in contact with VAL 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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60A VAL 3.8 1.2 - - - +
61A TRP* 3.2 7.0 - - - -
62A VAL* 2.7 46.4 + - + +
64A ALA 5.8 0.2 - - - +
80A LEU* 3.9 20.2 - - + -
114A VAL* 3.8 25.4 - - + +
115A ASP* 1.3 77.0 - - - +
117A GLU* 1.3 65.0 - - - +
118A GLY 3.8 0.6 + - - +
137A LEU* 3.7 27.8 - - + -
139A VAL* 4.2 16.4 - - + -
141A LYS 3.5 10.5 - - - +
142A ILE* 4.1 14.1 - - + -
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Residues in contact with GLU 117 (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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59A VAL* 4.0 22.1 - - + +
60A VAL 3.6 4.5 - - - +
61A TRP* 3.5 51.4 + - + +
116A VAL* 1.3 69.9 - - - +
118A GLY* 1.3 51.6 + - - +
140A GLN* 2.8 46.1 + - - +
141A LYS* 3.0 47.6 + - + +
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Residues in contact with GLY 118 (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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58A GLU 3.9 0.2 - - - +
59A VAL* 3.6 6.8 - - - +
60A VAL 3.0 31.0 + - - +
116A VAL* 3.8 4.0 + - - +
117A GLU* 1.3 74.0 - - - +
119A VAL* 1.3 64.2 + - - +
137A LEU* 3.7 20.1 - - - +
138A HIS 3.2 14.8 - - - -
139A VAL* 4.1 2.9 - - - -
140A GLN* 4.1 2.0 - - - -
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Residues in contact with VAL 119 (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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57A ASP* 4.3 7.4 - - - +
58A GLU 3.4 16.2 - - - +
59A VAL* 4.2 13.9 - - + -
118A GLY* 1.3 73.5 - - - +
120A VAL* 1.3 71.4 + - - +
121A ARG* 3.4 24.3 + - + +
137A LEU* 3.7 3.7 - - - +
138A HIS* 2.8 46.4 + - + +
140A GLN* 3.2 35.4 - - + +
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Residues in contact with VAL 120 (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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51A LEU* 3.6 31.2 - - + -
52A THR 4.1 3.4 - - - +
55A LYS* 3.3 28.7 - - + +
56A ALA* 3.9 4.9 - - - -
57A ASP* 2.5 35.4 + - - +
58A GLU 3.2 7.6 + - - +
60A VAL* 3.8 15.5 - - + -
119A VAL* 1.3 68.4 - - - +
121A ARG* 1.3 56.7 + - - +
135A VAL* 3.6 41.7 - - + -
136A GLU 3.7 5.8 - - - +
137A LEU* 4.4 5.6 - - + -
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Residues in contact with ARG 121 (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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57A ASP* 4.2 13.2 - - - +
96A HIS* 3.8 23.0 + - - -
119A VAL* 3.4 23.5 + - + +
120A VAL* 1.3 76.0 - - - +
122A LYS* 1.3 67.5 + - - +
135A VAL* 3.6 4.1 - - - -
136A GLU* 3.0 44.8 + - + +
138A HIS* 3.2 47.5 + - + +
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Residues in contact with LYS 122 (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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53A ILE* 3.7 33.6 - - + +
56A ALA* 4.8 8.0 - - + +
57A ASP* 5.1 2.4 + - - -
121A ARG* 1.3 75.5 - - - +
123A VAL* 1.3 72.5 + - - +
124A ASN* 4.2 3.0 + - - +
134A ASP 3.9 10.5 + - - +
135A VAL* 4.1 5.2 - - - +
136A GLU* 5.8 0.3 - - - +
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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