Contacts of the strand formed by residues 43 - 51 (chain H) in PDB entry 3T30
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 43 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G THR* 2.9 40.8 + - - +
118G GLN* 4.0 0.4 - - - +
32H PHE* 5.0 0.7 - - - -
41H SER* 5.7 3.6 - - - -
42H CYS* 1.3 85.5 + - - +
44H LEU* 1.3 60.0 + - - +
45H LEU* 3.8 7.4 + - + -
97H GLN* 2.9 54.4 + - + +
98H LEU 3.4 6.1 - - - +
99H SER* 3.3 18.5 + - - -
100H PRO* 4.4 0.7 - - - -
118H GLN 3.8 0.3 - - - +
119H GLU* 3.6 2.9 - - - -
120H ARG* 2.9 43.3 + - + +
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Residues in contact with LEU 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H TRP* 4.0 31.4 - - + -
32H PHE* 4.0 42.0 - - + -
43H ARG* 1.3 71.0 - - - +
45H LEU* 1.3 75.2 + - - +
46H LEU* 3.5 9.7 + - + +
97H GLN* 3.5 0.3 - - - -
98H LEU* 2.8 47.0 + - + +
102H VAL* 4.3 8.1 - - + -
104H PHE* 3.9 31.0 - - + -
118H GLN 3.7 6.3 - - - +
119H GLU* 4.7 2.7 - - + +
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Residues in contact with LEU 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H THR* 6.5 0.2 - - + -
43H ARG* 4.6 8.1 - - + -
44H LEU* 1.3 73.1 - - - +
46H LEU* 1.3 59.5 - - - +
47H HIS* 4.0 15.0 - - + +
95H GLY 6.2 0.7 - - - +
96H VAL 3.3 6.3 - - - +
97H GLN* 3.4 40.4 - - + +
117H GLY* 3.0 7.4 - - - -
118H GLN* 2.8 65.4 + - + +
120H ARG* 4.5 26.2 - - + -
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Residues in contact with LEU 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H TRP* 4.1 11.0 - - + -
44H LEU* 3.5 5.3 + - + -
45H LEU* 1.3 70.7 - - - +
47H HIS* 1.3 62.7 + - - +
48H THR 4.6 1.1 - - - +
49H ILE* 4.5 7.9 - - + -
64H ILE* 5.6 0.7 - - + -
80H ILE* 4.2 18.8 - - + -
93H MET* 3.0 53.2 - - + +
94H VAL* 3.9 2.3 + - - -
96H VAL* 2.9 27.1 + - + +
98H LEU* 4.2 22.0 - - + -
104H PHE* 4.3 4.9 - - + -
115H LEU* 4.0 26.0 - - + -
116H SER 3.7 15.7 - - - +
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Residues in contact with HIS 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18H LEU* 5.4 3.4 - - + +
45H LEU* 4.0 17.9 - - + +
46H LEU* 1.3 77.8 - - - +
48H THR* 1.3 69.3 + - + +
92H SER* 3.4 1.2 + - - -
93H MET* 2.8 31.0 + - - +
94H VAL* 3.6 19.6 + - + +
95H GLY 5.2 1.8 - - - -
116H SER* 2.8 20.3 + - - +
117H GLY* 3.6 12.7 + - - -
118H GLN* 3.0 44.4 + - + +
95I GLY 5.4 0.8 + - - -
96I VAL* 3.7 42.5 - - + +
98I LEU* 5.8 0.2 - - - +
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Residues in contact with THR 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46H LEU* 4.6 0.2 - - - +
47H HIS* 1.3 90.6 - - + +
49H ILE* 1.3 66.7 + - - +
50H CYS* 3.6 5.1 - - - -
90H MET* 3.8 11.2 - - + -
91H VAL 3.3 10.8 - - - +
92H SER* 4.1 8.5 - - - +
93H MET* 4.9 0.7 - - - +
115H LEU* 3.4 3.3 - - - +
116H SER* 2.9 45.5 + - - +
79I THR 3.9 0.9 + - - -
80I ILE* 3.0 32.6 + - + +
93I MET* 3.9 25.1 - - + -
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Residues in contact with ILE 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46H LEU* 4.5 6.1 - - + -
48H THR* 1.3 79.5 - - - +
50H CYS* 1.3 63.7 + - - +
62H VAL* 4.3 10.3 - - + -
80H ILE* 3.8 29.8 - - + -
81H ALA* 3.9 17.9 - - + -
83H LEU* 3.5 13.1 - - + +
90H MET* 3.2 3.6 - - - +
91H VAL* 2.9 38.9 + - + -
93H MET* 4.0 18.6 - - + -
113H VAL* 3.4 26.0 - - + -
114H PHE 3.2 7.4 - - - +
115H LEU* 3.7 21.5 - - + -
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Residues in contact with CYS 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48H THR* 3.6 19.1 - - - -
49H ILE* 1.3 79.7 - - - +
51H LEU* 1.3 64.3 + - - +
83H LEU* 4.3 0.7 - - - -
89H PRO 3.5 5.2 - - - -
90H MET* 3.7 11.7 - - - -
113H VAL* 3.5 5.9 - - - -
114H PHE* 2.9 34.5 + - - +
79I THR* 4.0 16.2 - - + -
80I ILE 3.7 1.3 - - - -
81I ALA* 3.6 33.0 - - - -
82I SER* 3.3 17.9 - - - +
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Residues in contact with LEU 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50H CYS* 1.3 71.9 - - - +
52H GLY* 1.3 68.2 + - - +
55H ALA* 4.5 4.5 - - + -
60H HIS* 3.7 30.5 - - + +
83H LEU* 4.0 14.6 - - + -
84H GLN* 3.5 17.0 - - - +
85H ALA* 3.3 37.9 - - + +
89H PRO* 2.7 26.6 + - + +
112H PRO 3.8 2.7 - - - +
113H VAL* 3.7 26.0 - - + -
114H PHE* 4.4 1.6 - - - -
59I MET* 3.6 6.2 - - + +
82I SER* 2.8 24.9 + - - -
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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