Contacts of the strand formed by residues 41 - 53 (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 PHE 41 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40D GLY* 1.3 73.2 - - - +
42D ALA* 1.3 80.9 + - - +
76D THR* 3.6 13.7 - - - -
77D PRO 3.0 27.8 - - - -
79D MET* 3.2 43.5 - - + -
164D THR* 5.3 0.4 + - - -
188D HIS* 3.7 24.5 - + - -
189D ALA* 3.8 10.1 - - - -
190D MET* 3.1 55.0 - - + -
193D ILE* 4.0 9.0 - - + -
194D PHE* 4.1 2.2 - - + -
310D ARG* 3.5 6.4 - - - +
311D PHE* 2.7 35.6 + - - +
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Residues in contact with ALA 42 (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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41D PHE* 1.3 102.3 - - - +
43D GLY* 1.3 60.1 + - - +
76D THR* 4.1 2.9 - - - +
77D PRO* 4.6 1.4 - - - +
79D MET* 3.5 24.0 - - - +
146D THR* 4.1 5.0 - - + +
162D MET* 4.1 19.5 - - + -
308D LEU* 3.8 16.2 - - + -
309D VAL 3.3 12.8 - - - +
310D ARG* 4.2 1.8 - - + -
311D PHE* 4.2 5.2 - - - -
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Residues in contact with GLY 43 (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* 1.3 75.9 - - - +
44D TYR* 1.3 70.1 + - - -
74D ILE* 3.9 9.0 - - - -
75D GLU 3.1 14.4 - - - -
76D THR* 4.0 2.5 - - - -
77D PRO* 5.3 0.7 - - - -
308D LEU* 3.1 9.0 - - - +
309D VAL* 2.8 35.3 + - - -
311D PHE* 4.2 2.4 - - - -
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Residues in contact with TYR 44 (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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43D GLY* 1.3 76.5 - - - -
45D LYS* 1.3 65.3 - - - +
46D ALA 3.5 0.3 + - - -
74D ILE* 3.7 3.3 - - - +
75D GLU* 2.9 38.7 + - + +
77D PRO* 5.4 2.7 - - + -
146D THR* 2.6 32.7 + - + -
147D VAL 5.4 0.7 - - - -
148D PRO* 3.3 26.8 - - + +
151D VAL* 4.4 16.6 - - + -
154D VAL* 4.0 25.8 - - + -
156D LYS* 4.3 14.6 - - + -
160D ASP* 2.4 33.0 + - - -
287D TYR* 4.1 3.5 + - - +
306D LYS 3.4 22.7 - - - +
307D ARG 3.5 2.2 - - - +
308D LEU* 4.0 22.7 - - + -
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Residues in contact with LYS 45 (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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2717A C 2.8 13.9 + - - -
2718A C 2.8 26.1 + - - -
43D GLY 4.2 0.8 + - - -
44D TYR* 1.3 70.5 - - - +
46D ALA* 1.3 60.6 + - - +
47D GLY* 4.2 6.5 - - - +
48D MET* 5.6 3.1 - - - -
72D THR* 4.1 24.2 + - + +
74D ILE* 4.1 13.2 - - + -
287D TYR* 3.2 9.4 - - - -
301D VAL* 3.2 19.6 + - + +
302D PRO 4.3 3.4 - - - +
303D GLY 2.8 30.4 + - - +
304D PRO 3.5 18.4 - - - +
305D ASP* 3.7 14.6 - - - +
306D LYS 2.8 24.4 + - - +
307D ARG 3.1 12.9 + - - +
309D VAL* 4.3 11.5 - - + +
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Residues in contact with ALA 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D TYR 4.4 2.0 - - - +
45D LYS* 1.3 74.7 - - - +
47D GLY* 1.3 59.5 + - - +
73D VAL* 2.9 21.9 + - + +
75D GLU* 4.6 2.5 - - + -
284D PHE* 3.7 9.9 - - + +
285D VAL 5.1 0.3 - - - +
287D TYR* 3.4 52.2 - - + +
290D VAL* 4.1 15.7 - - + -
305D ASP* 3.1 15.0 - - - +
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Residues in contact with GLY 47 (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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45D LYS* 4.2 4.2 - - - +
46D ALA* 1.3 82.1 - - - +
48D MET* 1.3 60.7 + - - -
72D THR* 3.2 8.8 - - - +
73D VAL* 2.5 33.4 + - - +
284D PHE* 4.0 13.4 - - - -
305D ASP* 3.6 12.2 + - - -
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Residues in contact with MET 48 (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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2717A C 3.6 23.1 - - - +
2718A C 3.8 21.1 - - - +
2719A A 2.8 52.9 + - + +
2764A C 5.9 0.7 - - - +
45D LYS* 5.6 2.9 - - - -
47D GLY* 1.3 74.2 - - - -
49D THR* 1.3 63.9 + - - +
70D PRO* 4.1 15.0 - - + -
71D VAL 3.2 13.5 - - - +
72D THR* 3.3 20.9 - - + +
73D VAL* 4.6 0.9 - - - +
284D PHE* 4.0 4.3 - - - -
299D GLY 3.2 28.7 - - - +
300D SER* 4.6 2.0 - - - +
335D ASN* 3.0 25.5 + - - +
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Residues in contact with THR 49 (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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2719A A 3.3 18.5 - - - +
48D MET* 1.3 75.1 - - - +
50D HIS* 1.3 66.4 + - - +
71D VAL* 2.9 30.7 + - - +
73D VAL* 4.2 13.5 - - - +
278D PRO 4.3 6.1 + - - +
280D VAL* 3.0 37.2 - - + -
284D PHE* 4.0 7.0 - - + -
296D LEU* 5.5 1.2 - - - +
330D VAL* 4.8 6.1 - - - +
331D SER* 3.6 21.7 + - - +
333D GLU 5.2 0.4 - - - +
335D ASN* 4.4 2.0 - - - +
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Residues in contact with HIS 50 (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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2719A A 2.7 43.4 + + + +
2720A C 4.5 4.0 - - - -
49D THR* 1.3 78.6 + - - +
51D VAL* 1.3 65.1 + - - +
52D VAL* 5.7 3.4 - - + -
68D THR* 3.6 27.6 - - + -
69D VAL 3.2 13.9 - - - +
71D VAL* 5.1 0.7 - - - -
329D TYR* 5.7 1.7 - + - -
330D VAL* 3.9 1.0 - - - +
331D SER* 3.0 51.0 + - - -
333D GLU* 5.2 2.7 - - - -
14V GLU* 4.5 2.9 - - + -
15V PRO 2.7 29.6 + - - -
16V GLY* 3.4 11.3 + - - -
17V THR* 4.1 10.1 - - - -
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Residues in contact with VAL 51 (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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50D HIS* 1.3 77.3 - - - +
52D VAL* 1.3 63.7 + - - +
53D LEU* 3.3 19.7 + - + -
67D GLU 3.6 0.2 - - - +
68D THR* 3.6 2.3 - - - -
69D VAL* 2.8 38.9 + - + +
71D VAL* 3.4 28.3 - - + -
270D ILE* 4.4 7.4 - - + -
296D LEU* 5.3 5.2 - - + -
327D VAL* 3.1 30.7 - - + -
329D TYR* 2.8 22.0 - - - +
330D VAL* 3.9 9.4 - - + -
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Residues in contact with VAL 52 (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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50D HIS* 5.7 2.5 - - + -
51D VAL* 1.3 75.7 - - - +
53D LEU* 1.3 70.1 + - - +
66D GLU* 4.1 28.0 - - + +
67D GLU 3.4 21.1 - - - +
68D THR* 4.8 13.7 - - + +
328D ARG* 2.9 27.1 + - + -
329D TYR* 2.6 46.5 + - + +
15V PRO* 4.9 13.0 - - + -
16V GLY 5.7 0.2 - - - +
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Residues in contact with LEU 53 (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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51D VAL* 3.3 25.4 - - + -
52D VAL* 1.3 90.4 - - - +
54D VAL* 1.3 67.8 + - - +
65D MET 3.4 0.2 - - - +
66D GLU* 3.4 5.2 - - - -
67D GLU* 2.7 43.0 + - + +
69D VAL* 4.1 23.8 - - + -
268D ARG* 5.2 6.3 - - - +
270D ILE* 3.6 34.5 - - + -
325D PRO* 4.8 10.8 - - + -
326D GLU 3.5 9.0 - - - +
327D VAL* 3.7 18.4 - - + -
328D ARG* 5.3 0.4 - - - -
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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