Contacts of the strand formed by residues 401 - 407 (chain A) in PDB entry 2HD5
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 ILE 401 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A THR* 3.8 24.0 - - + -
236A ARG 5.6 2.0 - - - +
237A GLU* 5.4 8.3 - - + +
323A LEU* 2.8 33.9 + - + +
324A PHE* 3.5 35.0 - - + +
348A TRP 5.0 0.2 - - - +
399A PRO* 3.5 15.8 - - - +
400A LYS* 1.3 88.1 - - + +
402A LEU* 1.3 62.5 + - - +
403A VAL* 3.9 10.2 + - + -
451A TYR* 3.3 24.2 - - + +
517A PHE* 4.7 0.9 - - + -
518A TYR 3.4 6.7 - - - +
519A GLU* 4.0 21.3 - - + +
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Residues in contact with LEU 402 (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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347A PHE* 4.1 16.8 - - + -
349A ASP* 5.6 0.2 - - - -
350A LEU* 4.2 7.9 - - + -
395A ILE* 5.9 1.1 - - + -
398A PHE* 5.6 0.7 - - + -
399A PRO* 3.9 20.9 - - + -
400A LYS 4.1 0.6 - - - -
401A ILE* 1.3 73.2 - - - +
403A VAL* 1.3 64.0 + - - +
404A LEU* 3.6 36.2 + - + -
431A LEU* 4.5 3.4 - - + -
433A LEU* 3.3 34.5 - - + -
448A TYR* 3.5 31.2 - - + -
516A LEU 3.5 2.3 - - - +
518A TYR* 2.8 38.1 + - + +
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Residues in contact with VAL 403 (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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300A LEU* 4.0 18.8 - - + -
301A ARG* 5.7 0.2 - - - +
324A PHE* 3.7 36.3 - - + -
348A TRP 4.3 5.2 + - - +
349A ASP* 3.2 18.2 - - + +
350A LEU 3.0 24.8 + - - -
401A ILE* 3.9 3.0 + - + -
402A LEU* 1.3 77.5 - - - +
404A LEU* 1.3 63.9 + - - +
515A LEU* 3.9 26.2 - - + -
516A LEU 3.3 7.9 - - - +
517A PHE* 3.8 24.5 - - + -
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Residues in contact with LEU 404 (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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350A LEU* 3.5 21.8 - - + -
352A LEU* 4.1 18.6 - - + -
360A LEU* 3.7 35.2 - - + -
364A MET* 4.5 7.6 - - + -
402A LEU* 3.6 33.2 - - + -
403A VAL* 1.3 77.5 - - - +
405A HIS* 1.3 61.1 + - - +
406A LEU* 4.0 1.7 + - + -
431A LEU* 4.1 9.2 - - + -
514A TYR 3.8 0.7 - - - +
515A LEU* 3.4 5.5 - - - -
516A LEU* 2.8 50.0 + - + +
518A TYR* 3.9 19.7 - - + -
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Residues in contact with HIS 405 (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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297A GLN* 3.4 40.2 - - + +
349A ASP* 4.6 4.9 - - - +
350A LEU 2.8 15.1 + - - +
351A SER* 2.8 25.7 + - - +
352A LEU 2.7 32.3 + - - +
404A LEU* 1.3 73.9 - - - +
406A LEU* 1.3 60.0 + - - +
407A LYS* 3.5 0.7 + - + -
409A PHE* 4.4 5.4 - + - -
514A TYR* 2.8 50.8 + + - -
515A LEU* 3.5 16.8 - - + -
42B ARG* 3.8 4.0 - - - -
70B VAL* 3.7 21.5 - - + -
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Residues in contact with LEU 406 (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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352A LEU* 3.8 15.9 - - + +
354A ILE* 4.4 5.4 - - + -
360A LEU* 4.3 23.6 - - + -
363A CYS* 4.9 5.6 - - - -
404A LEU 5.0 1.1 - - - +
405A HIS* 1.3 74.3 - - - +
407A LYS* 1.3 60.1 + - - +
408A ARG* 2.8 36.1 + - + +
425A VAL* 4.1 25.8 - - + +
427A PHE* 5.6 0.7 - - + -
513A ALA* 3.5 28.5 - - + +
514A TYR* 3.0 36.5 + - - +
516A LEU* 4.7 16.4 - - + -
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Residues in contact with LYS 407 (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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351A SER* 3.4 34.1 - - - -
352A LEU 2.9 27.3 + - - +
353A PRO* 4.3 7.2 - - + -
354A ILE* 3.8 14.0 + - - +
405A HIS* 4.5 0.9 - - - +
406A LEU* 1.3 69.2 - - - +
408A ARG* 1.3 55.2 + - - +
409A PHE* 2.8 33.7 + - + +
421A LEU* 4.0 4.0 - - - +
6B LYS* 3.1 20.5 + - - +
7B THR 2.9 20.2 + - - +
8B LEU* 3.8 27.1 - - + +
68B HIS* 4.6 2.9 - - - +
69B LEU 2.8 29.8 + - - +
70B VAL* 4.0 13.2 - - + -
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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