Contacts of the strand formed by residues 317 - 321 (chain C) in PDB entry 3DLX
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 MET 317 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312C GLU 3.7 15.7 - - - +
313C PHE* 3.9 14.8 - - - -
314C GLU* 3.0 51.8 + - + +
315C ASP 3.2 1.6 + - - -
316C GLY* 1.3 78.0 - - - +
318C TYR* 1.3 73.5 + - - +
319C ALA* 3.9 3.0 + - + +
339C VAL* 3.7 6.1 - - + +
340C HIS* 2.9 27.4 + - - +
395C ASP* 3.6 18.4 - - + +
396C LEU* 4.0 32.8 - - + -
436C LYS* 6.1 2.7 - - + -
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Residues in contact with TYR 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316C GLY 3.5 14.1 - - - -
317C MET* 1.3 70.9 - - - +
319C ALA* 1.3 57.9 + - - +
340C HIS* 3.3 38.7 + + + +
342C GLN* 6.0 0.9 - - + -
348C LEU* 4.0 9.0 - - + -
393C HIS 4.2 6.5 - - - +
394C VAL* 4.1 4.9 - - + -
395C ASP* 2.8 53.4 + - - +
396C LEU 3.3 2.6 + - - -
40D THR* 4.8 9.6 + - - -
263D GLN* 2.7 40.7 + - + +
264D ILE* 3.5 56.5 - - + -
267D HIS* 6.6 0.2 - + - -
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Residues in contact with ALA 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313C PHE* 3.8 30.5 - - + -
317C MET* 3.9 3.3 - - - -
318C TYR* 1.3 73.7 - - - +
320C ASN* 1.3 59.8 + - - +
321C LEU* 4.7 3.4 - - + -
339C VAL* 4.2 5.6 - - + -
340C HIS 3.0 6.7 + - - -
341C LEU* 3.4 17.0 - - + +
342C GLN* 2.8 27.4 + - - +
394C VAL* 4.1 3.4 - - - -
396C LEU* 3.2 19.3 - - + +
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Residues in contact with ASN 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319C ALA* 1.3 74.1 - - - +
321C LEU* 1.3 74.0 + - - +
322C GLY* 4.0 1.6 + - - -
342C GLN* 3.1 38.6 + - + +
343C SER* 4.2 0.4 - - - +
344C GLU* 3.9 15.7 + - - +
394C VAL* 3.7 11.5 - - + +
396C LEU 2.9 10.4 + - - +
397C THR* 3.4 5.4 - - + +
398C MET 3.1 24.8 + - - -
429C LEU* 3.5 44.2 - - + +
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Residues in contact with LEU 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313C PHE* 3.7 31.0 - - + -
319C ALA* 4.3 3.6 + - + -
320C ASN* 1.3 82.0 + - - +
322C GLY* 1.3 66.4 + - - +
326C PRO 3.4 25.4 - - - +
327C LEU* 3.6 18.6 - - + +
330C SER* 3.8 26.5 - - - +
341C LEU* 3.9 23.5 - - + +
342C GLN 4.4 3.4 + - - -
366C ALA* 5.7 4.7 - - - +
398C MET* 3.6 28.9 - - + +
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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