Contacts of the strand formed by residues 316 - 326 (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 VAL 316 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A ASN 3.1 10.8 + - - +
84A ASN 4.0 10.5 - - - +
85A CYS 4.3 1.3 - - - +
86A VAL* 4.0 9.6 - - + -
105A LEU* 3.1 12.7 - - - +
107A LYS* 2.8 39.7 + - + +
182A ILE* 3.5 25.6 - - + -
229A LEU* 4.3 4.7 - - + -
230A VAL 3.3 7.2 - - - +
231A SER* 4.1 4.5 - - - +
310A GLU* 3.5 37.2 - - + -
315A PHE* 1.3 78.5 - - - +
317A ALA* 1.3 68.0 + - - +
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Residues in contact with ALA 317 (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* 4.7 0.4 - - + -
107A LYS* 3.9 0.9 - - - -
124A THR* 3.8 10.5 - - + +
142A VAL* 3.6 31.2 - - + +
143A ILE* 3.9 23.3 - - + -
146A ALA* 3.8 11.7 - - + +
228A VAL 3.8 0.3 - - - +
229A LEU* 3.4 2.9 - - - -
230A VAL 2.9 32.3 + - - -
316A VAL* 1.3 75.7 - - - +
318A GLN* 1.3 60.7 + - - +
319A PHE* 5.0 0.4 - - + -
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Residues in contact with GLN 318 (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 VAL 4.7 3.2 - - - +
87A CYS* 5.8 3.6 - - - +
107A LYS* 3.6 28.4 - - + +
109A ASP* 3.6 26.5 + - - +
122A ALA* 3.4 21.3 - - + +
123A HIS* 3.6 3.8 - - - -
124A THR* 2.7 35.3 + - - +
146A ALA* 4.8 0.2 - - - -
227A ASP* 2.9 29.7 + - - +
228A VAL 3.0 13.7 - - - +
229A LEU* 3.8 18.0 - - + +
317A ALA* 1.3 76.8 - - - +
319A PHE* 1.3 73.9 + - - +
320A LYS* 3.7 5.3 - - - +
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Residues in contact with PHE 319 (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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122A ALA 3.5 4.5 - - - +
123A HIS* 3.5 35.0 - + - -
124A THR* 3.6 23.8 - - - -
143A ILE* 3.7 14.1 - - + -
146A ALA* 3.7 11.4 - - + +
147A HIS* 3.6 59.2 - + + -
150A ALA* 4.0 19.1 - - + +
226A VAL 4.0 1.0 - - - +
227A ASP* 3.9 0.2 - - - -
228A VAL* 2.9 34.5 + - + +
318A GLN* 1.3 79.2 - - - +
320A LYS* 1.3 61.0 + - - +
321A PHE* 5.1 2.5 - - + -
336A GLY* 5.7 2.9 - - - -
338A PHE* 3.8 16.6 - + + -
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Residues in contact with LYS 320 (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 PHE* 5.5 6.9 - - - -
109A ASP* 2.9 34.7 + - - +
120A ASN* 3.8 31.6 - - + +
121A VAL* 3.5 13.6 - - - +
122A ALA* 3.0 36.2 + - + +
225A ALA* 4.7 6.7 - - + -
226A VAL 3.1 19.3 - - - +
227A ASP* 3.3 36.4 + - + +
318A GLN* 3.7 3.8 - - - +
319A PHE* 1.3 76.0 - - - +
321A PHE* 1.3 68.3 + - - +
335A SER* 4.9 1.6 - - - -
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Residues in contact with PHE 321 (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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120A ASN 3.9 1.6 - - - -
150A ALA* 3.6 32.1 - - + -
153A ALA 4.2 0.4 - - - -
154A LEU* 3.8 39.7 - - + -
157A VAL* 6.1 0.4 - - + -
224A TYR 3.7 0.2 - - - +
225A ALA* 3.4 1.8 - - - -
226A VAL* 2.8 72.9 + - + -
228A VAL* 5.7 0.2 - - + -
319A PHE* 5.1 1.8 - - + -
320A LYS* 1.3 78.6 - - - +
322A THR* 1.3 63.3 + - - +
323A VAL* 4.0 18.4 - - + -
332A ARG* 3.8 26.2 - - + +
334A THR* 3.3 25.1 - - - +
335A SER* 4.7 3.1 - - - -
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Residues in contact with THR 322 (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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118A ILE 3.9 3.6 - - - +
119A ALA* 4.4 0.4 - - - -
120A ASN* 2.8 40.7 + - - +
190A LEU* 3.7 21.9 - - + +
223A VAL* 3.8 11.2 - - + -
224A TYR 3.3 9.6 - - - +
225A ALA* 4.0 4.0 - - - +
321A PHE* 1.3 75.5 + - - +
323A VAL* 1.3 63.3 + - - +
324A LEU* 4.6 0.2 - - + -
332A ARG* 3.5 4.7 - - - +
333A ILE* 2.9 54.6 + - + -
334A THR* 2.8 10.0 + - - -
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Residues in contact with VAL 323 (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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154A LEU* 4.5 9.2 - - + -
157A VAL* 4.3 15.0 - - + +
222A GLU 4.3 0.2 - - - +
223A VAL* 3.4 6.1 - - - +
224A TYR* 2.9 52.9 + - + +
226A VAL* 4.2 5.6 - - + -
321A PHE* 4.0 21.3 - - + -
322A THR* 1.3 76.0 - - - +
324A LEU* 1.3 67.9 + - - +
325A LEU* 4.1 6.1 + - + +
330A PRO* 3.7 31.0 - - + -
331A MET 3.5 15.0 - - - +
332A ARG* 4.0 3.6 - - - +
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Residues in contact with LEU 324 (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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12A ILE* 3.9 24.5 - - + -
18A VAL* 4.1 14.1 - - + +
21A TYR* 4.1 17.9 - - + -
222A GLU 4.0 4.0 - - - -
223A VAL* 4.0 24.2 - - + -
322A THR* 4.6 0.2 - - + -
323A VAL* 1.3 78.5 - - - +
325A LEU* 1.3 61.2 + - - +
326A MET* 3.0 15.1 + - + +
330A PRO* 3.5 0.2 - - - +
331A MET* 2.8 62.3 + - + +
333A ILE* 3.9 34.1 - - + -
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Residues in contact with LEU 325 (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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12A ILE* 3.9 2.4 - - - +
157A VAL* 3.4 29.6 - - + +
158A LYS* 4.4 2.7 - - - -
159A PRO* 4.2 18.2 - - + -
218A PHE* 3.8 26.9 - - + -
219A GLU 3.6 22.9 - - - +
220A VAL* 3.7 1.8 - - - -
221A HIS* 2.8 31.7 + - - -
222A GLU 2.9 22.4 + - - +
224A TYR* 4.0 18.4 - - + -
323A VAL* 4.3 10.1 - - + +
324A LEU* 1.3 71.7 - - - +
326A MET* 1.3 64.8 + - - +
329A GLY 5.0 0.2 - - - -
330A PRO* 4.2 16.8 - - + -
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Residues in contact with MET 326 (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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12A ILE* 3.8 29.4 - - - +
18A VAL* 3.9 31.4 - - + -
159A PRO* 5.0 4.3 - - - +
220A VAL* 4.1 4.6 - - - +
324A LEU* 3.0 18.7 + - + +
325A LEU* 1.3 74.6 - - - +
327A PRO* 1.4 82.2 - - + +
328A ASN* 4.2 7.0 - - + +
329A GLY* 2.9 26.0 + - - +
331A MET* 4.0 24.0 - - + -
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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