Contacts of the strand formed by residues 117 - 126 (chain A) in PDB entry 3J2I
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 PHE 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A GLN* 3.6 29.6 - - + -
17A VAL* 3.4 29.6 - - + -
20A LYS* 3.9 28.7 - - + +
21A TYR* 3.5 50.6 - + + +
24A GLY* 5.6 1.6 - - - -
112A VAL 3.9 0.3 - - - +
113A HIS* 3.2 3.2 - - - -
114A VAL* 3.0 41.9 + - - +
115A ASP* 3.6 4.9 - - - -
116A GLY* 1.3 76.3 - - - +
118A ILE* 1.3 60.6 - - - +
119A ALA* 4.0 0.5 + - - +
192A GLN* 3.4 49.8 - - + +
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Residues in contact with ILE 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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21A TYR* 3.1 27.1 + - - -
75A ALA* 3.7 12.3 - - + -
112A VAL 3.5 3.8 - - - -
113A HIS* 4.1 4.0 - - + -
116A GLY 3.6 11.4 + - - +
117A PHE* 1.3 73.4 - - - +
119A ALA* 1.3 63.2 + - - +
120A ASN* 3.5 34.8 - - - +
190A LEU* 3.4 22.6 - - + +
191A LYS 4.3 2.8 + - - +
194A VAL 3.7 13.2 - - - +
195A ILE* 3.6 41.1 - - + +
276A MET* 4.0 25.6 - - + -
322A THR* 3.9 1.6 - - - +
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Residues in contact with ALA 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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21A TYR* 4.2 2.0 - - - +
24A GLY* 3.7 8.7 - - - +
25A GLY* 3.4 36.8 - - - +
28A ALA* 3.9 6.4 - - - +
111A GLY* 3.3 1.9 - - - -
112A VAL 2.8 36.3 + - - +
117A PHE 4.0 0.6 + - - -
118A ILE* 1.3 73.0 - - - +
120A ASN* 1.3 62.9 + - - +
322A THR* 4.0 3.8 - - - -
333A ILE* 3.9 14.4 - - + -
334A THR* 4.0 4.7 - - + -
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Residues in contact with ASN 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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75A ALA* 4.3 0.2 - - - +
76A PHE* 4.2 5.3 - - - +
109A ASP* 6.0 0.2 - - - -
110A LEU 3.6 3.8 - - - +
111A GLY* 3.3 19.6 - - - -
118A ILE* 3.5 24.0 - - - +
119A ALA* 1.3 73.1 - - - +
121A VAL* 1.3 60.3 + - - +
190A LEU* 4.3 2.0 - - - +
195A ILE* 3.7 25.0 + - - +
225A ALA* 3.8 18.1 - - + +
320A LYS* 3.8 25.8 - - + +
321A PHE 3.9 1.7 - - - -
322A THR* 2.8 22.7 + - - +
334A THR* 2.8 19.7 + - - -
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Residues in contact with VAL 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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28A ALA* 4.0 15.3 - - + +
29A ASN* 4.2 1.3 - - - +
32A LEU* 3.7 29.8 - - + -
108A ILE 4.1 0.2 - - - +
109A ASP* 3.4 2.7 - - - +
110A LEU* 3.0 59.9 + - + +
120A ASN* 1.3 75.5 - - - +
122A ALA* 1.3 66.2 + - - +
320A LYS* 3.5 17.9 - - - +
334A THR* 3.7 9.2 - - + -
335A SER 3.6 30.3 - - - +
336A GLY 4.2 0.7 - - - +
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Residues in contact with ALA 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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32A LEU* 5.1 0.2 - - - -
108A ILE 3.1 13.5 - - - +
109A ASP* 3.7 8.7 - - - +
121A VAL* 1.3 82.2 - - - +
123A HIS* 1.3 63.3 + - - +
318A GLN* 3.4 35.9 - - + +
319A PHE* 3.5 5.7 - - - +
320A LYS* 3.0 39.5 + - + +
336A GLY 4.9 3.1 + - - -
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Residues in contact with HIS 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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32A LEU* 3.7 23.6 - - + -
36A VAL* 3.9 22.2 - - + +
106A VAL 3.7 0.9 - - - +
107A LYS* 3.3 3.5 - - - -
108A ILE* 2.9 30.8 + - - +
122A ALA* 1.3 77.1 - - - +
124A THR* 1.3 79.9 + - - +
125A PHE* 4.0 14.4 - + - +
318A GLN* 3.6 4.9 + - - -
319A PHE* 3.5 15.5 - + - -
336A GLY* 3.5 12.0 - - - -
337A PRO* 3.5 50.0 + - + +
338A PHE* 3.8 10.1 - + + -
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Residues in contact with THR 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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105A LEU* 3.6 37.5 - - + -
106A VAL 3.2 4.7 - - - +
107A LYS* 3.5 6.4 - - - +
123A HIS* 1.3 91.0 + - - +
125A PHE* 1.3 67.0 + - - +
143A ILE* 3.9 18.3 - - + +
317A ALA* 4.1 5.2 - - + -
318A GLN 2.7 39.4 + - - -
319A PHE* 3.6 18.5 - - - -
338A PHE* 5.2 0.7 - - - -
343A TYR* 4.2 6.9 + - - -
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Residues in contact with PHE 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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36A VAL* 3.9 25.1 - - + -
39A SER* 3.4 37.7 - - - -
105A LEU* 3.5 3.5 - - - -
106A VAL* 2.8 58.9 + - + +
108A ILE* 3.7 25.4 - - + -
123A HIS* 4.0 21.5 - + - +
124A THR* 1.3 81.2 - - - +
126A VAL* 1.3 77.2 - - - +
127A VAL* 4.5 10.1 - - + -
342A LEU* 6.5 0.9 - - + -
343A TYR* 3.9 12.3 - - - +
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Residues in contact with VAL 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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103A GLY* 3.6 30.1 - - - +
104A ASP 3.2 4.0 - - - +
105A LEU* 4.5 2.9 - - - -
125A PHE* 1.3 90.5 - - - +
127A VAL* 1.3 66.4 + - - +
128A ASP 3.4 2.6 + - - -
129A VAL* 3.7 32.0 + - + +
135A VAL* 4.0 24.2 - - + -
139A LYS* 4.2 15.9 - - + +
143A ILE* 3.8 22.9 - - + -
342A LEU* 6.2 1.0 - - - +
343A TYR* 4.3 4.4 + - + +
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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