Contacts of the strand formed by residues 331 - 334 (chain I) 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 ARG 331 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140I ILE* 3.3 48.3 + - + +
141I HIS* 4.8 0.4 - - - +
142I ARG* 3.6 10.8 - - - +
143I SER 3.6 4.3 - - - +
325I ILE 3.5 11.7 - - - +
326I ASP* 3.3 38.8 + - - +
327I HIS 3.0 11.5 + - - +
328I LEU* 2.8 29.2 - - + +
329I GLY 3.3 0.8 - - - -
330I ASN* 1.3 79.6 - - - +
332I ARG* 1.3 61.0 + - - +
333I ILE* 5.6 0.5 - - - +
412I ALA* 4.8 2.8 - - - +
426I ASP 4.9 0.6 + - - -
427I VAL* 3.7 35.4 + - - +
434I HIS* 5.5 7.7 - - - -
465I GLY 4.6 1.4 - - - +
466I PHE* 3.9 8.5 - - - -
467I ILE* 5.3 2.4 + - - +
38R G 3.1 22.9 + - - +
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Residues in contact with ARG 332 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140I ILE* 3.1 14.6 - - - +
141I HIS* 3.0 42.2 + - + +
143I SER* 3.6 15.0 - - - +
144I PRO* 3.6 28.5 - - - -
165I LEU* 4.6 9.5 - - - +
272I ALA* 3.9 8.6 - - - +
331I ARG* 1.3 73.8 - - - +
333I ILE* 1.3 72.5 + - - +
334I ARG* 3.3 34.4 - - - +
335I THR* 5.8 0.6 + - - -
338I GLU* 3.2 26.1 + - - +
463I ALA 3.9 3.0 + - - -
464I LEU* 2.8 37.7 + - - +
465I GLY* 3.5 19.4 - - - +
466I PHE* 4.0 3.4 - - + -
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Residues in contact with ILE 333 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21I ILE* 6.1 0.7 - - + -
138I SER* 3.9 23.3 - - - +
139I GLN 3.2 17.9 - - - +
140I ILE* 3.7 13.5 - - + -
331I ARG 5.6 0.2 - - - +
332I ARG* 1.3 101.8 + - - +
334I ARG* 1.3 67.2 + - - +
335I THR* 3.5 14.9 + - + +
338I GLU* 5.7 0.2 - - - +
410I ILE* 3.7 23.6 - - + -
438I ILE* 5.6 2.0 - - + -
461I VAL* 4.1 13.9 - - + -
465I GLY* 3.0 22.7 + - - +
467I ILE* 3.7 29.8 - - + -
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Residues in contact with ARG 334 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138I SER* 3.5 6.6 - - - -
139I GLN* 2.9 62.1 + - + +
140I ILE 5.0 0.2 - - - +
141I HIS* 3.5 27.6 - - + +
165I LEU* 5.2 11.2 - - - +
166I PRO* 3.7 31.8 - - - +
332I ARG* 3.3 25.6 - - - +
333I ILE* 1.3 71.0 - - - +
335I THR* 1.3 62.7 + - - +
338I GLU* 3.6 36.5 + - - +
339I LEU* 3.9 22.1 - - + +
342I ASP* 4.0 23.4 + - - +
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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