Contacts of the strand formed by residues 359 - 364 (chain C) in PDB entry 2HU4
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 GLY 359 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355C LYS* 3.5 1.2 - - - +
356C TYR 2.8 32.0 + - - -
357C GLY 4.0 1.6 - - - +
358C ASN* 1.3 81.7 - - - +
360C VAL* 1.3 70.3 + - - +
378C TRP* 3.8 9.2 - - - -
379C ASP 3.5 3.6 - - - -
380C PRO* 3.8 5.2 - - - -
381C ASN 3.3 16.7 - - - +
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Residues in contact with VAL 360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C ILE* 4.5 7.4 - - + -
353C SER* 5.1 2.7 - - - -
354C PHE 3.1 12.1 - - - +
355C LYS* 4.1 0.7 - - - -
359C GLY* 1.3 79.7 - - - +
361C TRP* 1.3 61.0 + - - +
362C ILE* 3.8 28.0 - - + -
377C ILE 3.4 2.1 - - - +
378C TRP* 3.2 19.0 - - - -
379C ASP* 3.2 25.6 + - + +
382C GLY* 4.1 16.6 - - - +
383C TRP* 3.0 44.9 - - + -
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Residues in contact with TRP 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C ILE* 3.6 29.5 + - + +
95C ASN* 3.7 28.9 - - - -
96C GLY* 4.6 1.6 - - - -
97C TRP* 3.3 44.2 - + + -
353C SER* 3.2 9.2 - - - -
354C PHE* 2.8 36.6 + - + +
356C TYR* 4.0 14.5 - + - -
360C VAL* 1.3 72.5 - - - +
362C ILE* 1.3 60.5 + - - +
363C GLY 4.1 0.2 + - - -
376C MET* 3.8 29.0 - - + +
377C ILE 3.4 15.5 - - - -
378C TRP* 3.5 54.7 - + + -
392C VAL* 4.6 15.0 - - + -
395C GLN* 5.0 4.3 - - + -
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Residues in contact with ILE 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C ILE* 4.9 7.2 - - + -
319C SER* 4.2 11.4 - - - +
321C VAL* 3.6 34.3 - - + +
323C GLY* 4.4 13.9 - - - -
352C PHE 5.3 0.2 - - - +
353C SER* 3.7 14.4 - - - +
360C VAL* 3.8 25.6 - - + -
361C TRP* 1.3 76.1 - - - +
363C GLY* 1.3 70.6 + - - +
364C ARG* 4.1 14.9 + - + +
375C GLU 3.6 1.4 - - - +
376C MET* 3.5 5.8 - - - -
377C ILE* 2.7 49.2 + - + +
379C ASP* 4.8 6.5 - - + -
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Residues in contact with GLY 363 (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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300C ARG* 4.9 5.2 + - - -
323C GLY* 4.3 5.4 - - - +
351C GLY* 5.5 0.3 - - - -
352C PHE* 4.0 25.1 + - - +
361C TRP 4.1 1.0 + - - -
362C ILE* 1.3 77.4 - - - +
364C ARG* 1.3 64.0 + - - +
374C PHE* 3.8 14.0 - - - -
375C GLU 3.5 7.6 - - - -
376C MET* 3.7 16.0 - - - +
407C SER* 5.0 3.1 + - - -
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Residues in contact with ARG 364 (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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321C VAL* 3.3 18.4 - - - +
322C PHE 2.9 27.1 + - - -
323C GLY* 3.8 20.0 - - - +
327C ARG* 3.5 26.2 - - - +
330C ASP* 2.9 40.2 + - - -
362C ILE* 4.4 5.8 - - + -
363C GLY* 1.3 77.0 - - - +
365C THR* 1.3 65.6 + - - +
374C PHE* 3.1 17.6 - - - -
375C GLU* 3.0 60.6 + - + +
377C ILE* 3.6 14.3 - - + +
390C PHE* 5.5 1.4 - - - -
394C LYS* 4.7 3.6 - - - +
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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