Contacts of the strand formed by residues 308 - 313 (chain D) in PDB entry 1NJI
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 LEU 308 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22D GLU* 4.7 3.9 + - + +
23D THR* 3.6 25.8 - - + +
24D PRO* 4.0 17.8 - - + +
42D ALA* 3.8 19.7 - - + -
43D GLY 3.1 22.2 - - - +
44D TYR* 4.0 21.9 - - + -
146D THR* 4.2 4.9 - - + -
156D LYS* 5.2 3.0 - - - +
160D ASP* 3.7 23.1 - - + +
162D MET* 3.2 30.7 - - + -
204D GLY* 4.5 1.2 - - - -
306D LYS 3.7 1.6 + - - -
307D ARG* 1.3 86.9 - - + +
309D VAL* 1.3 66.0 + - - +
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Residues in contact with VAL 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D ALA* 3.3 6.2 - - - +
43D GLY 2.8 47.5 + - - +
45D LYS* 4.3 11.9 - - + +
74D ILE* 3.5 30.3 - - + -
202D VAL* 4.1 7.4 - - + -
203D ALA 3.6 12.6 - - - +
204D GLY* 4.7 2.9 - - - -
301D VAL* 3.6 24.9 - - + -
302D PRO 3.9 10.8 - - - +
307D ARG* 4.3 8.5 - - + +
308D LEU* 1.3 80.1 - - - +
310D ARG* 1.3 62.4 + - - +
311D PHE* 4.4 3.7 - - + -
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Residues in contact with ARG 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2672A C 4.4 4.4 + - - -
24D PRO* 3.4 34.3 + - + +
25D ARG* 3.7 3.4 - - - +
26D PHE* 3.4 52.8 - - + +
29D TRP* 4.0 4.2 - - - -
40D GLY* 6.0 0.8 - - - -
41D PHE 3.5 11.4 - - - +
42D ALA* 4.2 2.0 - - + -
162D MET* 3.1 55.5 - - + +
163D GLU 3.4 16.0 + - - -
164D THR* 3.3 20.0 + - - +
201D ASP 3.4 1.4 - - - +
202D VAL* 3.2 8.2 - - - +
203D ALA* 2.9 37.8 + - + +
309D VAL* 1.3 77.8 - - - +
311D PHE* 1.3 61.6 + - - +
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Residues in contact with PHE 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D PHE* 3.7 6.5 - - - -
40D GLY* 3.1 4.9 - - - -
41D PHE 2.7 44.8 + - - +
42D ALA* 4.2 1.6 - - - -
43D GLY 4.2 7.6 - - - -
74D ILE* 3.5 35.0 - - + -
76D THR* 3.7 24.2 - - + -
190D MET* 4.2 10.5 - - + -
194D PHE* 3.8 19.7 - - + -
200D ALA* 4.5 3.1 - - + -
201D ASP 3.6 2.7 - - - -
202D VAL* 4.0 20.2 - - + -
269D LEU* 4.3 17.0 - - + -
295D THR* 4.5 6.1 - - + -
297D VAL* 3.7 24.9 - - + -
309D VAL* 4.4 5.4 - - + -
310D ARG* 1.3 76.1 - - - +
312D ARG* 1.3 63.6 + - - +
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Residues in contact with ARG 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2807A U 2.6 30.1 + - - -
26D PHE* 3.4 39.6 - - + +
27D ASN 4.4 0.8 - - - +
28D SER* 2.7 35.3 + - - +
29D TRP* 4.8 2.2 - - + -
30D PRO* 4.1 11.7 - - + -
39D GLN 3.9 6.3 - - - +
194D PHE* 3.7 5.2 - - - -
200D ALA* 3.1 4.7 - - - -
201D ASP* 2.6 85.8 + - - +
263D THR* 3.8 7.9 + - - +
265D LEU* 4.5 2.4 - - - +
311D PHE* 1.3 77.6 - - - +
313D PRO* 1.3 80.7 - - + +
315D VAL* 3.5 18.5 - - - +
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Residues in contact with PRO 313 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30D PRO* 3.1 31.0 - - + +
38D VAL 5.4 0.2 - - - +
39D GLN* 3.4 29.8 - - + +
193D ILE* 4.8 8.5 - - + +
194D PHE* 3.8 22.4 - - + -
199D TYR 4.0 3.8 - - - +
312D ARG* 1.3 88.5 - - + +
314D ALA* 1.3 71.4 + - - +
315D VAL 3.2 1.7 + - - -
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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