Contacts of the strand formed by residues 317 - 326 (chain D) in PDB entry 4XLN
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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219D GLU* 6.3 0.2 - - + -
238D PRO* 3.1 13.4 - - - +
264D LEU* 4.0 13.9 - - + -
269D LEU* 5.7 2.2 - - + -
283D PHE* 4.1 18.4 - - + -
313D LEU* 3.1 23.3 - - + +
314D PRO* 3.7 26.9 + - + -
315D ARG 3.4 0.8 - - - -
316D HIS* 1.3 91.9 - - + +
318D THR* 1.3 76.2 + - - +
337D LEU* 3.6 34.1 - - + -
339D TRP* 3.5 46.0 - - + -
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Residues in contact with THR 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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236D TYR 4.1 2.2 - - - -
237D ARG* 5.1 0.7 - - - -
238D PRO* 3.7 24.5 - - + -
313D LEU* 4.7 1.6 - - - -
316D HIS 5.3 1.8 - - - +
317D MET* 1.3 89.6 - - - +
319D ALA* 1.3 64.7 + - - +
320D LYS* 4.7 7.5 - - - -
337D LEU* 3.7 4.2 - - - +
338D GLU* 2.9 52.5 + - - +
339D TRP* 5.5 1.6 - - - -
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Residues in contact with ALA 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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235D ALA* 3.3 22.4 - - - +
236D TYR* 3.1 27.9 + - + +
313D LEU* 3.7 14.1 - - + -
318D THR* 1.3 79.3 - - - +
320D LYS* 1.3 68.5 + - - +
335D LEU* 5.0 9.2 - - + -
336D PHE 3.9 5.2 - - - -
337D LEU* 3.6 18.4 - - + -
338D GLU 5.1 0.2 - - - +
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Residues in contact with LYS 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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234D GLU 4.9 1.3 - - - -
235D ALA* 4.5 9.2 - - + -
318D THR* 4.7 7.2 - - - -
319D ALA* 1.3 81.7 - - - +
321D GLU* 1.3 70.9 + - + +
322D VAL 3.7 0.9 - - - -
335D LEU* 4.0 3.4 - - - +
336D PHE* 2.9 39.6 + - + +
338D GLU* 3.2 38.5 + - + +
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Residues in contact with GLU 321 (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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220D ARG* 5.7 1.0 - - - -
234D GLU* 4.6 3.2 + - - +
235D ALA* 5.4 0.8 - - - +
320D LYS* 1.3 83.4 - - + +
322D VAL* 1.3 67.2 + - - +
323D GLU* 3.5 4.0 + - - +
334D THR 3.6 7.6 - - - +
335D LEU* 3.9 0.6 - - - -
336D PHE* 3.5 35.7 + - + +
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Residues in contact with VAL 322 (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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230D TRP* 4.7 3.6 - - + -
233D LYS 3.8 13.9 - - - +
234D GLU* 3.1 47.5 + - + +
320D LYS 3.7 0.2 - - - -
321D GLU* 1.3 75.2 - - - +
323D GLU* 1.3 73.0 + - - +
324D ALA* 4.1 8.2 + - + +
333D LEU* 3.6 22.7 - - + -
334D THR 4.1 2.0 - - - -
335D LEU* 4.5 8.3 - - + -
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Residues in contact with GLU 323 (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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321D GLU 4.5 2.0 - - - +
322D VAL* 1.3 80.9 - - - +
324D ALA* 1.3 62.5 + - - +
325D GLU* 5.6 2.7 - - + -
332D HIS 3.7 1.0 - - - +
333D LEU* 3.2 11.6 - - - +
334D THR* 2.9 64.7 + - - +
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Residues in contact with ALA 324 (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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230D TRP* 3.8 29.8 - - + -
322D VAL* 4.1 6.6 + - + +
323D GLU* 1.3 74.7 + - - +
325D GLU* 1.3 60.7 + - - +
326D GLU 4.2 1.1 + - - -
331D VAL* 4.8 1.8 - - + -
333D LEU* 3.9 6.3 - - + -
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Residues in contact with GLU 325 (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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224D ARG* 5.3 1.9 + - - -
323D GLU* 5.5 3.6 - - + +
324D ALA* 1.3 73.6 - - - +
326D GLU* 1.3 61.7 + - - +
327D GLU* 3.5 23.1 - - - +
331D VAL* 3.7 2.1 - - - +
332D HIS* 2.9 66.2 + - + +
334D THR* 6.0 0.4 - - - +
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Residues in contact with GLU 326 (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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227D LEU* 3.4 28.9 - - + +
324D ALA* 4.2 1.4 + - + -
325D GLU* 1.3 75.0 - - - +
327D GLU* 1.3 61.6 + - - +
328D GLY* 3.1 31.4 + - - +
330D SER 4.0 1.3 - - - +
331D VAL* 3.6 25.1 - - + -
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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