Contacts of the strand formed by residues 70 - 74 (chain D) in PDB entry 3SRF
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 70 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46D ILE 3.2 3.6 + - - -
47D ILE* 3.4 31.2 - - + -
48D CYS 2.9 26.5 + - - -
68D MET* 3.7 8.3 - - - +
69D ASN* 1.3 86.5 - - + +
71D ALA* 1.3 62.3 + - - +
108D ALA* 3.6 23.1 - - + +
110D ALA* 3.9 26.2 - - + -
238D MET* 4.1 18.4 - - + -
357D CYS* 5.9 0.7 - - - -
463D HIS* 3.9 21.1 - - + +
464D LEU* 5.5 1.3 - - + +
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Residues in contact with ALA 71 (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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48D CYS 3.5 4.5 - - - -
50D ILE* 3.9 21.5 - - + -
68D MET* 4.1 9.2 - - - -
70D VAL* 1.3 71.2 - - - +
72D ARG* 1.3 61.5 + - - +
73D LEU* 3.8 5.9 + - + +
90D VAL* 3.9 29.2 - - + -
107D VAL* 4.3 2.1 - - + +
108D ALA 2.8 14.8 + - - +
109D VAL* 3.6 2.8 - - - -
110D ALA 2.8 26.8 + - - +
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Residues in contact with ARG 72 (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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47D ILE* 3.8 15.5 - - + -
48D CYS 2.7 15.8 + - - +
49D THR* 2.5 51.6 + - - +
50D ILE* 3.1 26.3 + - - +
70D VAL 3.8 1.2 + - - -
71D ALA* 1.3 71.6 - - - +
73D LEU* 1.3 67.9 + - - +
74D ASN* 3.7 24.2 + - - +
110D ALA* 3.6 5.8 - - - +
112D ASP* 2.9 37.1 + - + -
240D PHE* 3.9 16.2 - - + -
269D LYS* 4.5 0.8 - - - +
359D MET* 3.6 31.3 - - - +
361D SER* 3.5 12.9 - - - -
534D PYR 3.9 17.4 + - - +
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Residues in contact with LEU 73 (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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50D ILE* 4.7 6.5 - - + +
71D ALA* 3.9 19.7 - - + +
72D ARG* 1.3 79.1 - - - +
74D ASN* 1.3 60.3 + - - +
75D PHE* 3.8 16.5 + - + -
83D HIS* 3.6 34.8 - - + +
86D THR* 3.8 26.0 - - + -
87D ILE* 3.5 29.6 - - + -
90D VAL* 4.9 3.6 - - + -
109D VAL* 4.1 17.5 - - + -
110D ALA 2.8 13.8 + - - +
111D LEU* 3.8 0.4 - - - -
112D ASP* 2.9 27.5 + - - +
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Residues in contact with ASN 74 (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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49D THR* 4.6 8.2 - - + +
50D ILE 5.4 2.8 + - - +
72D ARG* 3.7 30.6 + - - +
73D LEU* 1.3 70.5 - - - +
75D PHE* 1.3 61.3 + - - +
76D SER* 3.3 21.5 + - - -
77D HIS* 3.3 18.4 + - - +
83D HIS* 3.1 21.1 - - - -
112D ASP* 3.9 6.1 - - - +
532D K 3.2 21.7 - - - -
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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