Contacts of the strand formed by residues 48 - 53 (chain C) in PDB entry 4ERQ
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 VAL 48 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44C HIS* 3.9 20.6 - - + -
46C LYS 4.3 0.2 - - - +
47C ALA* 1.3 76.1 - - - +
49C SER* 1.3 59.2 + - - +
50C SER 4.2 4.9 - - - +
51C VAL* 4.5 0.2 - - + -
62C SER* 4.2 9.0 - - - -
63C SER 3.3 16.8 - - - +
64C SER* 4.2 0.9 - - - -
305C ILE* 3.1 19.3 - - - +
319C ALA* 3.5 24.0 - - + -
320C ALA 3.2 15.2 + - - +
321C LEU* 3.9 5.7 - - - +
325C LYS* 3.6 29.8 - - - +
326C THR 4.4 0.9 - - - +
327C ILE* 4.0 22.2 - - + -
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Residues in contact with SER 49 (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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47C ALA 3.9 0.4 + - - -
48C VAL* 1.3 73.8 - - - +
50C SER* 1.3 60.9 + - - +
63C SER* 2.7 27.3 + - - -
64C SER* 4.7 1.1 - - - -
90C ILE 2.6 29.1 + - - -
91C SER* 3.5 15.6 - - - -
263C PHE* 3.5 5.4 - - - -
305C ILE* 3.6 16.5 - - - +
306C SER* 3.8 0.7 - - - -
321C LEU* 5.5 1.1 - - - -
5338F CYS* 4.1 13.7 - - - -
5340F ARG* 3.4 25.6 - - - +
5341F SER* 5.6 1.3 - - - -
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Residues in contact with SER 50 (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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48C VAL* 3.8 1.4 - - - +
49C SER* 1.3 84.3 + - - +
51C VAL* 1.3 64.6 + - - +
52C LYS* 3.8 12.0 + - - +
61C ALA 3.9 0.2 - - - +
62C SER* 3.2 4.3 - - - -
63C SER* 2.9 39.3 + - - +
91C SER 3.9 0.2 - - - -
92C ASP* 2.9 32.0 + - - -
93C VAL* 3.9 6.6 + - - +
263C PHE* 3.4 13.1 - - - -
306C SER* 3.6 8.8 + - - -
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Residues in contact with VAL 51 (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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48C VAL* 4.5 0.2 - - + -
50C SER* 1.3 78.8 - - - +
52C LYS* 1.3 75.9 + - - +
60C LEU* 4.1 11.9 - - + -
61C ALA 3.3 5.2 - - - +
62C SER* 3.8 19.1 - - - -
306C SER* 3.1 25.7 + - - +
307C THR 4.5 0.9 - - - +
308C ALA* 3.3 12.6 - - + +
317C ALA* 4.0 30.5 - - + +
319C ALA* 4.0 19.1 - - + -
327C ILE* 4.0 18.2 - - + -
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Residues in contact with LYS 52 (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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50C SER* 3.8 12.8 - - - +
51C VAL* 1.3 82.0 - - - +
53C PHE* 1.3 60.0 + - - +
60C LEU* 3.4 5.9 - - - +
61C ALA 2.9 32.6 + - - +
92C ASP* 3.1 17.2 + - - -
93C VAL* 2.8 41.1 + - + +
94C ALA* 4.4 10.2 - - - +
95C TRP* 3.1 22.8 + - + +
135C CYS 4.6 2.8 + - - -
136C ASN* 4.7 7.3 + - - +
263C PHE* 3.9 20.2 - - - -
307C THR 6.0 0.9 - - - -
308C ALA* 4.2 7.4 - - + -
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Residues in contact with PHE 53 (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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52C LYS* 1.3 73.7 - - - +
54C SER* 1.3 65.0 + - - +
55C PRO* 3.6 2.6 - - - +
57C GLY* 5.4 0.7 - - - -
59C TRP 3.5 12.8 - - - -
60C LEU* 3.8 12.8 - - + -
74C ALA* 4.1 13.0 - - + -
95C TRP* 3.5 9.5 - - - -
308C ALA* 3.5 26.1 - - + +
309C CYS 3.5 7.9 - - - +
310C HIS* 3.4 49.4 - + - -
311C PRO* 3.9 19.0 - - + +
315C ILE* 3.9 25.1 - - + -
317C ALA* 3.7 24.9 - - + -
329C LEU* 4.1 7.4 - - + -
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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