Contacts of the strand formed by residues 116 - 124 (chain B) in PDB entry 3AA6
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 VAL 116 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49B ILE* 3.9 22.9 - - + -
58B ASP* 3.7 51.1 - - + +
59B TYR 4.0 0.9 - - - +
60B LEU* 3.5 30.7 - - + +
108B ARG* 3.4 8.7 - - - +
115B GLY* 1.3 79.3 - - - +
117B SER* 1.3 65.0 + - - +
134B ILE* 3.4 2.9 - - - +
135B LYS 2.9 32.6 + - - +
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Residues in contact with SER 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ASP 4.4 0.3 - - - +
60B LEU* 4.0 2.2 - - - -
75B TRP* 3.9 17.4 - - - -
101B ASN* 4.9 2.2 + - - -
104B PHE* 3.8 11.8 + - - +
105B ASP* 2.9 35.3 + - - +
108B ARG* 3.5 21.8 + - - +
116B VAL* 1.3 82.9 - - - +
118B SER* 1.3 69.3 + - - +
119B VAL* 6.0 0.2 - - - -
132B ILE* 6.2 0.2 - - - -
133B LEU 3.2 11.9 - - - -
134B ILE* 4.2 5.8 - - - -
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Residues in contact with SER 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B TYR* 3.5 8.5 - - - +
60B LEU* 3.0 32.1 + - - +
74B PRO* 3.8 4.4 - - - +
101B ASN* 3.6 7.4 - - - -
117B SER* 1.3 80.2 + - - +
119B VAL* 1.3 67.0 + - - +
120B TYR* 3.4 29.0 + - - -
131B VAL 3.7 1.2 - - - +
133B LEU* 2.8 40.5 + - - +
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Residues in contact with VAL 119 (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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74B PRO* 3.7 1.4 - - - +
97B GLU* 3.5 6.9 - - - +
100B ALA* 3.7 30.1 - - + +
101B ASN* 2.8 38.9 + - - +
104B PHE* 3.9 34.3 - - + -
117B SER* 6.0 0.2 - - - -
118B SER* 1.3 80.9 - - - +
120B TYR* 1.3 72.3 + - - +
121B LEU* 3.9 20.0 - - + -
131B VAL 3.2 9.2 - - - +
132B ILE* 4.1 16.8 - - + -
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Residues in contact with TYR 120 (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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59B TYR* 3.5 3.3 - - - -
60B LEU 2.7 28.1 + - - -
62B CYS* 5.1 0.4 - - - -
64B TYR* 4.7 8.1 - - + +
65B ASN* 3.1 34.6 + - + -
72B ARG* 3.3 38.6 - - - +
74B PRO* 3.5 29.1 - - + +
97B GLU* 3.4 2.9 - - - -
118B SER* 3.4 22.3 + - - -
119B VAL* 1.3 77.3 - - - +
121B LEU* 1.3 62.6 + - - +
122B TRP* 3.8 5.9 - - + -
130B GLY* 3.2 2.4 - - - -
131B VAL* 2.9 52.7 + - + -
133B LEU* 3.6 16.4 - - + -
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Residues in contact with LEU 121 (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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72B ARG* 3.8 8.8 + - - -
89B PRO* 4.2 10.2 - - - +
93B LEU* 3.7 23.6 - - + +
96B LEU* 3.8 27.6 - - + +
97B GLU* 2.8 57.8 + - + +
100B ALA* 5.0 3.4 - - + -
119B VAL* 3.9 15.9 - - + -
120B TYR* 1.3 76.5 - - - +
122B TRP* 1.3 66.0 + - - +
128B PHE* 4.5 9.9 - - + -
129B ALA 3.3 6.7 - - - +
130B GLY* 3.6 21.3 - - - -
132B ILE* 6.1 1.3 - - + -
154B VAL* 5.8 1.6 - - + -
213B ILE* 6.1 2.2 - - + -
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Residues in contact with TRP 122 (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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64B TYR* 3.4 45.3 - + + -
89B PRO* 5.5 2.5 - - + -
93B LEU* 3.2 9.6 - - - -
120B TYR* 3.8 7.9 - - + -
121B LEU* 1.3 82.0 - - - +
123B ASP* 1.3 72.4 + - - +
124B LEU* 4.0 4.0 - - + +
128B PHE* 3.4 4.2 - - - +
129B ALA* 2.9 60.6 + - + +
130B GLY* 3.7 27.6 - - - -
131B VAL* 3.9 2.2 - - + -
153B VAL* 4.4 5.2 - - + -
494C PRO* 3.7 21.5 - - + -
495C LYS 2.9 25.4 + - - -
496C MET* 3.6 41.1 - - + -
497C PRO* 5.8 0.2 - - + -
499C ARG* 6.1 0.2 - - - -
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Residues in contact with ASP 123 (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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88B MET 4.8 2.3 - - - +
89B PRO* 4.3 2.9 - - - +
90B SER* 3.5 40.4 + - - -
92B ARG* 5.3 3.5 + - - -
93B LEU* 3.5 17.2 - - - +
122B TRP* 1.3 87.6 - - - +
124B LEU* 1.3 64.4 + - - +
127B GLY 4.1 5.9 - - - +
496C MET* 5.5 0.9 - - - +
497C PRO* 6.1 1.0 - - - +
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Residues in contact with LEU 124 (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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122B TRP* 3.8 7.8 + - - +
123B ASP* 1.3 86.0 - - - +
125B ASP* 1.3 68.2 + - - +
126B HIS 3.3 0.4 - - - -
127B GLY 3.0 24.6 + - - +
128B PHE 3.4 29.2 - - - +
129B ALA* 3.9 7.4 - - + +
155B GLU* 3.8 19.7 - - + +
157B GLN* 3.6 24.5 - - - +
494C PRO* 4.4 7.0 - - + -
495C LYS 3.8 22.2 - - - +
497C PRO* 6.2 0.2 - - + -
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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