Contacts of the strand formed by residues 311 - 318 (chain A) in PDB entry 1LL9
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 SER 311 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258A ARG* 2.8 25.8 + - - -
273A MET* 4.5 7.0 - - - +
274A LEU 3.3 11.9 - - - -
276A TRP* 3.9 6.7 - - - +
308A VAL* 2.6 26.9 + - - +
309A ARG 2.9 4.6 + - - -
310A ALA* 1.3 74.2 - - - +
312A TRP* 1.3 60.3 + - - +
313A VAL* 3.7 17.5 - - - -
328A PHE 3.4 1.6 - - - +
329A ILE* 3.3 27.7 - - - +
330A PRO* 3.5 3.2 - - - +
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Residues in contact with TRP 312 (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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272A GLU 3.9 0.2 - - - +
273A MET* 3.3 3.5 - - - -
274A LEU* 2.8 29.7 + - + +
276A TRP* 3.5 32.5 - + + +
278A VAL* 3.6 26.7 - - + -
283A ILE* 3.8 26.4 - - + +
311A SER* 1.3 70.3 - - - +
313A VAL* 1.3 60.6 + - - +
314A HIS* 3.3 26.0 + + + +
325A TYR* 3.2 32.3 + + - -
327A ALA* 3.5 14.4 - - + -
328A PHE 3.7 3.6 - - - -
329A ILE* 3.9 10.5 - - + -
350A VAL* 4.9 1.3 - - + -
353A ALA* 4.2 2.9 - - + -
354A TRP* 3.9 30.3 - + - -
357A LEU* 3.7 33.7 - - + -
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Residues in contact with VAL 313 (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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256A GLN* 4.1 13.2 - - + +
271A TRP* 3.8 28.3 - - + -
272A GLU 3.5 2.9 - - - -
273A MET* 3.6 23.3 - - + -
308A VAL 5.4 0.7 - - - +
311A SER* 4.0 13.0 - - - -
312A TRP* 1.3 73.4 - - - +
314A HIS* 1.3 65.0 + - - +
327A ALA* 3.0 3.6 - - - +
328A PHE* 2.8 78.7 + - + +
330A PRO* 4.2 5.6 - - + -
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Residues in contact with HIS 314 (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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265A MET* 5.5 1.0 - - - +
271A TRP* 3.6 7.6 - - - -
272A GLU* 2.9 62.4 + - + +
274A LEU* 3.6 22.9 - - + +
283A ILE* 4.6 9.4 - - + -
287A SER* 4.4 16.2 - - - -
312A TRP* 3.3 19.2 + + - +
313A VAL* 1.3 77.7 - - - +
315A LYS* 1.3 67.0 + - - +
316A THR* 5.6 2.7 - - + -
325A TYR* 2.7 32.7 + + + +
326A VAL 3.1 15.9 - - - +
327A ALA* 3.8 1.3 - - + -
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Residues in contact with LYS 315 (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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64A SER* 3.6 21.4 - - - +
65A VAL* 3.7 15.5 - - + +
67A LYS* 4.1 7.6 - - - -
68A THR* 3.7 21.5 - - + -
112A TYR* 4.5 0.9 - - - -
150A TYR* 2.9 40.7 + - - -
270A GLY 3.3 25.1 - - - +
271A TRP* 4.0 4.0 - - + -
272A GLU* 4.2 15.1 + - - +
314A HIS* 1.3 82.0 - - - +
316A THR* 1.3 94.7 + - - +
325A TYR* 3.4 3.8 - - - -
326A VAL* 3.0 27.1 + - + -
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Residues in contact with THR 316 (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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64A SER* 3.6 2.8 - - - -
65A VAL* 3.9 2.4 + - - -
287A SER* 4.6 16.9 + - - +
314A HIS* 5.4 3.4 - - + +
315A LYS* 1.3 108.1 + - - +
317A GLY* 1.3 58.9 + - - +
324A SER 3.6 6.3 - - - -
325A TYR* 3.4 26.7 - - + -
346A ASN* 3.6 35.5 + - + +
349A ARG* 5.2 1.6 - - - +
350A VAL* 4.7 1.1 - - + -
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Residues in contact with GLY 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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62A LEU 3.7 2.9 - - - -
64A SER* 3.6 17.0 - - - -
65A VAL 3.9 1.6 - - - -
316A THR* 1.3 78.0 - - - +
318A ALA* 1.3 61.3 + - - +
324A SER* 2.8 36.9 + - - -
349A ARG* 2.8 22.8 + - - +
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Residues in contact with ALA 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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61A GLU 6.1 0.2 - - - -
62A LEU 5.4 0.2 - - - -
63A GLY* 3.5 8.1 - - - -
64A SER* 3.6 11.1 + - - +
221A TYR* 5.1 2.9 - - - +
317A GLY* 1.3 76.8 - - - +
319A THR* 1.3 69.0 + - - +
322A PHE* 3.3 13.7 - - - +
343A ASN* 3.6 27.4 - - - +
346A ASN* 5.8 0.2 - - - +
349A ARG* 4.0 4.7 - - - +
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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