Contacts of the strand formed by residues 311 - 320 (chain D) in PDB entry 5LK5
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 311 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81D PHE* 3.4 10.3 - - + -
83D PRO* 3.0 23.9 - - - +
84D PHE* 2.7 54.2 + + + +
85D SER* 4.7 0.4 - - - -
86D ASN* 3.4 30.3 - - + -
91D LEU* 3.8 20.2 - - + -
112D LEU* 3.8 29.6 - - + -
113D PHE 3.6 4.3 - - - -
129D ASN* 3.4 30.5 - - + -
130D ILE* 3.9 6.3 - - + -
308D TYR* 3.6 26.9 - + + -
310D ASN* 1.3 75.8 - - - +
312D GLY* 1.3 57.8 + - - +
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Residues in contact with GLY 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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80D SER* 3.2 6.6 - - - -
81D PHE* 3.0 42.8 + - - +
83D PRO* 4.4 0.7 - - - -
113D PHE 2.9 7.5 + - - -
115D ASN* 3.7 24.4 - - - +
310D ASN* 3.5 2.6 + - - -
311D PHE* 1.3 73.0 - - - +
313D VAL* 1.3 66.8 + - - +
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Residues in contact with VAL 313 (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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78D SER* 3.4 34.1 - - - +
79D ALA 3.3 9.9 - - - +
80D SER* 4.1 10.3 - - - -
81D PHE* 3.6 6.1 - - - -
111D LYS 3.7 0.5 - - - +
112D LEU* 3.5 3.6 - - - +
113D PHE* 2.7 45.2 + - + +
114D PRO 4.6 7.4 - - - +
115D ASN* 4.7 6.1 - - - +
117D LEU* 4.1 21.3 - - + +
119D GLN* 4.1 17.3 - - + +
312D GLY* 1.3 84.9 - - - +
314D LEU* 1.3 63.7 + - - +
315D GLY 4.4 0.9 - - - +
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Residues in contact with LEU 314 (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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23D PHE* 4.7 12.6 - - + -
37D TRP* 4.1 15.8 - - + -
78D SER* 3.3 1.4 - - - -
79D ALA* 2.8 38.3 + - + +
81D PHE* 3.5 9.6 - - + -
93D VAL* 5.0 3.6 - - + -
94D GLN 6.2 0.2 - - - +
110D VAL* 4.1 22.9 - - + -
111D LYS 3.3 8.5 - - - +
112D LEU* 3.9 12.3 - - + -
313D VAL* 1.3 74.7 - - - +
315D GLY* 1.3 67.6 + - - +
316D LEU* 4.7 0.9 - - + +
330D PHE* 4.0 36.6 - - + -
331D LEU 6.2 0.2 - - - +
332D ILE* 3.8 26.5 - - + -
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Residues in contact with GLY 315 (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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77D LEU 3.6 7.2 - - - -
78D SER* 3.8 8.1 - - - -
110D VAL* 3.6 6.8 - - - +
111D LYS* 2.8 39.4 + - - +
113D PHE* 4.1 5.5 - - - -
122D MET* 4.1 12.3 - - - -
313D VAL 4.1 1.0 - - - -
314D LEU* 1.3 76.1 - - - +
316D LEU* 1.3 64.2 + - - -
317D ASP* 3.7 3.1 + - - -
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Residues in contact with LEU 316 (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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37D TRP* 4.1 13.7 - - + -
49D PHE* 3.9 32.5 - - + -
66D LEU* 3.7 30.3 - - + -
75D TYR 3.8 0.7 - - - -
76D ALA* 3.3 6.6 + - - -
77D LEU* 2.8 34.7 + - + +
109D TYR 4.2 9.0 - - - +
110D VAL* 3.8 28.3 - - + -
122D MET* 3.6 0.4 - - - +
314D LEU* 4.4 0.9 + - + -
315D GLY* 1.3 70.0 - - - -
317D ASP* 1.3 59.1 + - - +
318D LEU* 4.1 7.0 - - + -
327D PHE* 4.1 22.7 - - + -
330D PHE* 4.1 15.3 - - + -
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Residues in contact with ASP 317 (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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46D PHE* 5.4 1.6 - - - -
75D TYR 3.3 11.9 - - - +
76D ALA* 3.9 6.8 - - - +
109D TYR* 3.5 19.5 + - - -
111D LYS* 3.5 33.9 + - + +
113D PHE* 5.5 0.2 - - - -
122D MET* 4.0 18.4 - - + -
123D HIS* 3.2 39.2 - - - +
124D GLY* 3.2 14.8 + - - -
315D GLY 3.7 2.9 + - - -
316D LEU* 1.3 75.4 - - - +
318D LEU* 1.3 65.0 + - - +
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Residues in contact with LEU 318 (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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49D PHE* 5.2 0.9 - - + -
68D THR* 4.7 5.2 - - + -
73D ARG 4.0 0.2 - - - +
74D PHE* 3.3 9.1 - - - -
75D TYR* 2.7 53.2 + - + +
107D GLY* 3.8 24.5 - - - +
109D TYR* 3.6 40.4 - - + +
316D LEU* 4.5 8.5 - - + -
317D ASP* 1.3 82.8 + - - +
319D TRP* 1.3 61.1 + - - +
320D GLN* 4.0 20.4 - - + +
327D PHE* 3.9 23.1 - - + -
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Residues in contact with TRP 319 (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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72D ALA* 3.5 32.3 - - + -
73D ARG* 3.3 38.6 - - - -
74D PHE* 3.6 42.2 - + + -
105D CYS* 4.8 14.4 - - - -
106D GLY* 3.2 4.7 - - - -
107D GLY* 3.0 25.9 + - - +
109D TYR* 4.8 3.2 + - - +
318D LEU* 1.3 75.0 - - - +
320D GLN* 1.3 70.8 + - - +
321D VAL* 3.7 24.6 - - + +
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Residues in contact with GLN 320 (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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68D THR* 2.5 35.9 + - + +
70D GLN 5.2 0.4 - - - +
71D LYS 4.1 0.3 - - - -
72D ALA* 3.0 5.4 + - - -
73D ARG 3.0 31.9 + - - -
75D TYR* 4.2 12.6 - - + -
99D HIS* 4.5 0.2 - - - -
103D ILE* 3.7 12.4 - - + +
105D CYS 3.9 3.6 - - - -
106D GLY* 4.1 4.9 - - - -
107D GLY 3.1 20.8 + - - -
318D LEU* 4.0 10.8 - - + +
319D TRP* 1.3 85.1 - - - +
321D VAL* 1.3 65.7 + - - +
322D LYS 4.4 2.7 - - - +
323D SER* 3.6 11.4 - - - -
325D THR* 2.9 30.4 + - - +
327D PHE* 5.0 0.8 - - - -
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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