Contacts of the strand formed by residues 39 - 49 (chain D) in PDB entry 6I53
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 THR 39 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31D ARG* 3.2 15.1 + - - +
32D PRO* 3.0 26.1 + - + +
37D ARG* 5.8 0.4 - - - +
38D VAL* 1.3 70.9 - - - +
40D GLU* 1.3 60.3 + - - +
41D VAL* 3.4 15.5 + - + -
70D TRP* 4.3 13.7 - - + -
71D LYS 5.2 4.7 - - - +
95D TRP* 3.9 26.7 - - + -
166D GLU 2.8 15.6 + - - -
167D VAL* 3.4 10.7 - - - +
168D VAL 2.8 29.1 + - - +
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Residues in contact with GLU 40 (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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38D VAL* 3.7 12.1 + - + +
39D THR* 1.3 71.3 - - - +
41D VAL* 1.3 61.5 + - - +
42D LYS* 3.7 13.5 + - + +
69D SER 3.8 4.9 - - - +
70D TRP* 3.9 10.6 - - - +
71D LYS 4.9 1.6 + - - +
168D VAL* 3.4 16.4 - - + +
170D GLU* 2.9 42.5 - - + +
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Residues in contact with VAL 41 (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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39D THR* 3.9 22.9 - - + -
40D GLU* 1.3 70.7 - - - +
42D LYS* 1.3 62.2 + - - +
43D THR* 3.7 1.9 + - + -
68D GLN* 4.0 26.7 - - + +
69D SER 3.4 7.6 - - - +
70D TRP* 4.0 10.8 - - + -
95D TRP* 4.7 0.2 - - + -
97D PRO* 4.3 19.1 - - + -
167D VAL* 4.0 17.9 - - + -
168D VAL 2.9 7.0 + - - +
169D TYR* 3.4 30.8 - - + -
170D GLU* 3.0 27.1 + - - +
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Residues in contact with LYS 42 (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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40D GLU* 4.1 12.6 - - - +
41D VAL* 1.3 71.8 - - - +
43D THR* 1.3 63.3 + - - +
44D ASP* 5.2 0.5 - - - +
67D ARG 4.6 0.2 - - - -
68D GLN* 3.3 1.9 - - - -
69D SER* 2.5 50.0 + - - +
70D TRP* 5.8 0.7 - - - -
170D GLU* 3.3 35.4 - - + +
171D TRP 5.3 0.9 - - - +
172D THR* 3.6 25.2 - - + +
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Residues in contact with THR 43 (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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41D VAL* 4.3 0.9 - - + -
42D LYS* 1.3 75.8 - - - +
44D ASP* 1.3 66.0 + - - +
66D PHE* 4.6 4.0 - - + -
67D ARG 3.4 7.9 - - - +
68D GLN* 4.1 12.6 - - + +
157D PHE* 3.7 27.1 - - + -
169D TYR* 3.6 34.3 - - + -
170D GLU 2.8 20.4 + - - +
171D TRP* 3.5 21.9 - - - -
172D THR* 3.4 24.3 + - - -
213D MET* 4.3 2.4 - - - +
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Residues in contact with ASP 44 (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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42D LYS 5.2 0.7 - - - +
43D THR* 1.3 78.9 - - - +
45D ILE* 1.3 73.5 + - - +
65D PHE 4.4 0.2 - - - -
66D PHE* 3.7 0.3 - - - -
67D ARG* 2.7 71.3 + - + +
171D TRP* 4.5 6.9 - - - -
172D THR* 3.9 9.4 + - + +
173D ARG* 2.5 34.6 + - - -
178D SER* 2.9 24.2 - - - +
180D VAL* 5.5 0.5 - - - +
201E ALA* 5.1 0.3 - - - +
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Residues in contact with ILE 45 (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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44D ASP* 1.3 84.7 + - - +
46D PHE* 1.3 62.8 + - - +
47D VAL* 3.9 13.7 - - + -
64D VAL* 3.7 30.3 - - + -
65D PHE 3.9 2.9 - - - -
66D PHE* 3.8 21.1 - - + -
101D PHE* 5.5 1.8 - - + -
155D LEU* 4.6 18.4 - - + -
157D PHE* 3.6 31.0 - - + -
171D TRP* 3.9 15.9 - - + -
178D SER 3.0 20.7 + - - +
179D VAL* 3.4 17.1 - - + -
180D VAL* 3.3 11.8 + - - +
215D THR* 4.9 1.6 - - - +
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Residues in contact with PHE 46 (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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45D ILE* 1.3 73.1 - - - +
47D VAL* 1.3 59.1 + - - +
48D THR* 3.2 27.2 + - + +
65D PHE* 2.8 55.3 + + + -
67D ARG* 3.4 26.9 - - - +
180D VAL* 3.5 29.2 - - + -
181D VAL 4.6 2.9 - - - -
182D ALA* 4.1 24.9 - - + -
200E PHE* 3.5 30.1 - + - -
201E ALA* 6.4 1.3 - - + -
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Residues in contact with VAL 47 (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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45D ILE* 3.9 19.3 - - + -
46D PHE* 1.3 69.4 - - - +
48D THR* 1.3 62.4 + - - +
49D SER 3.9 1.1 - - - +
50D PHE* 3.9 25.6 - - + +
62D ILE* 3.7 39.7 - - + -
63D ASP 3.7 4.0 - - - +
64D VAL* 3.9 2.9 - - + -
179D VAL* 4.3 3.1 - - + -
180D VAL 2.9 10.9 + - - +
181D VAL* 3.6 24.4 - - + -
182D ALA* 2.9 28.2 + - - +
217D PHE* 4.1 13.5 - - + -
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Residues in contact with THR 48 (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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46D PHE* 3.2 28.5 + - + +
47D VAL* 1.3 73.1 - - - +
49D SER* 1.3 60.9 + - - -
63D ASP* 2.6 45.4 + - - +
64D VAL 4.8 0.2 - - - -
65D PHE* 3.7 37.5 - - + -
132D ARG* 6.0 0.2 - - - -
182D ALA* 3.4 18.7 - - - +
185D GLY* 3.4 9.6 - - - -
99E LEU* 4.7 12.5 + - + +
200E PHE* 5.4 0.4 - - + -
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Residues in contact with SER 49 (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 VAL* 3.4 3.3 - - - -
48D THR* 1.3 83.2 + - - +
50D PHE* 1.3 60.9 + - - +
51D GLY* 3.1 6.9 + - - -
62D ILE 4.0 0.2 - - - -
63D ASP* 3.1 31.9 + - - +
185D GLY* 3.3 15.3 - - - -
187D ARG* 3.1 47.4 + - - -
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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