Contacts of the strand formed by residues 122 - 128 (chain A) in PDB entry 2A4X
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 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A HIS* 3.5 36.5 - - + +
73A PHE* 4.0 13.8 + - - +
74A ALA* 3.2 8.5 - - + -
75A ILE* 3.1 21.8 + - - +
114A ILE* 3.6 17.9 - - + -
115A VAL 3.9 3.1 - - - -
116A LYS* 3.1 26.5 - - + +
120A GLY 4.8 1.3 - - - +
121A ASN* 1.3 74.4 - - - +
123A VAL* 1.3 65.0 + - - +
124A ASP* 3.9 2.2 - - - +
700A BLM 3.5 32.5 - - + -
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Residues in contact with VAL 123 (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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21A PHE* 4.0 13.7 - - + -
22A TYR* 3.9 22.0 - - + +
25A LEU* 4.0 13.0 - - + -
75A ILE* 3.2 17.9 - - + +
77A PHE* 3.6 26.2 - - + -
114A ILE* 3.5 2.7 - - - -
115A VAL* 3.0 46.2 + - + +
117A ASP* 4.2 2.2 - - + +
121A ASN* 4.0 11.2 - - + +
122A VAL* 1.3 79.8 - - - +
124A ASP* 1.3 67.1 + - - +
125A LEU* 4.0 6.2 + - + -
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Residues in contact with ASP 124 (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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74A ALA* 3.5 21.8 - - - +
75A ILE 2.9 6.6 + - - +
76A ALA* 3.4 19.3 - - + +
77A PHE* 2.8 27.0 + - - +
112A TYR* 3.1 35.3 + - + +
113A ALA 3.5 4.0 - - - -
114A ILE* 3.6 13.5 - - - +
122A VAL* 3.9 2.3 - - - +
123A VAL* 1.3 72.8 - - - +
125A LEU* 1.3 67.0 + - - +
126A PHE* 5.2 0.2 - - + -
700A BLM 3.2 26.8 - - - +
207B LEU* 5.5 2.3 - - - +
209B ALA* 5.8 0.5 - - - +
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Residues in contact with LEU 125 (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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25A LEU* 3.7 27.4 - - + -
77A PHE* 3.6 5.2 - - + -
79A PHE* 3.7 13.2 - - + -
85A VAL* 4.2 15.7 - - + +
88A LYS* 4.3 10.5 - - + -
89A TYR* 4.1 37.9 - - + +
92A LEU* 4.4 3.1 - - + -
111A ARG 3.9 0.2 - - - +
112A TYR* 3.4 2.9 - - - -
113A ALA* 2.9 38.9 + - + +
115A VAL* 4.3 22.2 - - + -
123A VAL* 4.2 13.2 - - + +
124A ASP* 1.3 81.1 - - - +
126A PHE* 1.3 64.0 + - - +
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Residues in contact with PHE 126 (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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76A ALA* 3.9 24.7 - - + -
77A PHE 2.9 34.6 + - - -
78A GLU* 3.4 27.2 - - + -
79A PHE* 2.7 36.1 + - - -
85A VAL* 3.6 5.2 - - - -
110A GLN* 3.5 22.9 - - - +
111A ARG 3.1 12.6 - - - +
112A TYR* 3.4 23.6 - + + -
125A LEU* 1.3 76.7 - - - +
127A ALA* 1.3 61.1 + - - +
128A PRO* 5.2 0.4 - - + -
700A BLM 3.0 36.3 - - - -
206B SER* 3.5 15.7 - - - -
207B LEU* 5.3 0.9 - - + -
248B ARG* 4.5 1.3 - - - -
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Residues in contact with ALA 127 (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 3.5 10.5 - - - +
81A ASP* 3.3 37.5 - - - +
82A THR 4.0 1.3 - - - +
85A VAL* 3.4 8.5 - - + -
110A GLN* 3.2 6.4 - - - -
111A ARG* 2.8 34.3 + - + -
126A PHE* 1.3 78.0 - - - +
128A PRO* 1.3 73.8 - - + +
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Residues in contact with PRO 128 (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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78A GLU* 3.9 18.8 - - + +
79A PHE 3.6 13.9 - - - +
80A PRO 4.3 11.8 - - - +
81A ASP* 5.1 2.9 - - - -
82A THR* 5.1 1.2 + - - -
109A GLY 4.1 5.4 - - - +
110A GLN* 4.4 9.2 - - + +
126A PHE* 4.7 2.0 - - + -
127A ALA* 1.3 91.0 - - + +
129A LEU* 1.3 64.9 + - - +
130A PRO* 3.1 21.3 - - + +
700A BLM 5.6 5.4 - - - +
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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