Contacts of the strand formed by residues 36 - 44 (chain K) in PDB entry 1UW9
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 ILE 36 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34K THR 3.8 13.7 - - - +
35K ASP* 1.3 71.6 - - - +
37K LEU* 1.3 66.9 + - - +
102K ALA* 3.5 1.6 - - - -
103K TYR* 2.8 37.4 + - + -
105K ILE* 4.1 8.3 - - - -
108K PHE* 3.6 38.4 - - + -
116K MET* 4.9 3.6 - - - -
120K ILE* 3.8 29.4 - - + -
138K LEU* 4.6 3.8 - - + -
139K ARG 3.5 10.3 - - - +
140K ILE* 4.9 7.9 - - + -
141K PRO* 3.7 19.7 - - + -
144K TYR* 4.2 22.9 - - + -
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Residues in contact with LEU 37 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31K VAL* 4.0 22.4 - - + -
35K ASP* 3.8 13.5 - - + -
36K ILE* 1.3 81.5 - - - +
38K ALA* 1.3 59.7 - - - +
85K TYR* 3.8 15.0 - - - +
101K VAL 3.3 4.3 - - - +
102K ALA* 3.8 22.7 - - + -
103K TYR* 5.1 0.2 - - - -
138K LEU* 3.1 10.3 - - - +
139K ARG* 2.7 73.8 + - + +
364K PHE* 3.7 23.3 - - + -
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Residues in contact with ALA 38 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37K LEU* 1.3 75.1 - - - +
39K ALA* 1.3 60.5 + - - +
40K PHE* 3.7 26.7 - - + -
99K ALA 3.6 1.2 - - - +
100K TYR* 3.4 5.5 - - - -
101K VAL* 2.9 32.0 + - + +
103K TYR* 3.8 16.8 - - + -
120K ILE* 4.2 1.6 - - + -
135K LEU* 3.8 4.7 - - + -
137K ASP 3.5 4.3 - - - -
138K LEU* 3.6 17.5 - - + -
364K PHE* 3.7 5.6 - - - -
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Residues in contact with ALA 39 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38K ALA* 1.3 72.9 - - - +
40K PHE* 1.3 62.0 + - - +
41K ARG 4.1 0.2 - - - -
98K ILE* 4.1 4.7 - - + -
99K ALA 3.8 3.1 - - - -
100K TYR* 3.9 9.9 - - + -
135K LEU* 3.7 2.8 - - - +
136K GLU* 2.8 30.3 + - + +
137K ASP 3.0 13.6 + - - +
363K TYR* 3.8 30.5 - - + -
364K PHE* 3.6 20.8 - - + -
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Residues in contact with PHE 40 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38K ALA* 3.7 16.8 - - + -
39K ALA* 1.3 70.8 - - - +
41K ARG* 1.3 59.8 + - - +
42K MET* 3.5 1.1 + - + -
57K VAL* 3.7 22.9 - - + -
97K TYR 3.3 1.7 - - - +
98K ILE* 3.2 7.0 - - - -
99K ALA* 2.8 49.3 + - + +
101K VAL* 4.0 15.7 - - + -
103K TYR* 3.6 18.8 - - - -
120K ILE* 3.5 36.8 - - + -
121K VAL* 5.0 0.2 - - + -
124K VAL* 4.5 0.4 - - + -
125K PHE* 4.1 9.4 - + - -
133K LEU* 3.8 43.3 - - + -
134K ARG 3.4 1.8 - - - -
135K LEU* 4.0 20.4 - - + -
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Residues in contact with ARG 41 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39K ALA 4.0 1.4 + - - -
40K PHE* 1.3 68.1 - - - +
42K MET* 1.3 60.5 + - - +
43K THR* 5.1 0.8 + - - +
90K VAL* 3.9 13.9 - - + +
96K GLN* 3.0 43.9 + - + +
97K TYR 3.4 4.0 - - - +
98K ILE* 3.9 16.2 - - + +
132K ALA 4.1 0.2 - - - +
133K LEU* 3.3 6.4 - - - -
134K ARG* 2.7 47.5 + - + +
136K GLU* 2.8 33.8 + - + +
305K ARG* 3.2 48.9 + - - +
306K ASN* 4.3 6.7 - - - +
363K TYR* 3.6 15.5 + - - -
474K LYS 5.0 0.2 + - - -
475K LEU* 3.2 24.0 + - - -
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Residues in contact with MET 42 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40K PHE* 4.2 5.6 - - - +
41K ARG* 1.3 73.8 - - - +
43K THR* 1.3 64.3 + - - +
44K PRO* 3.6 6.6 - - + +
50K PRO* 3.4 32.3 - - + +
53K CYS* 3.6 25.6 - - + +
54K GLY* 3.4 26.9 - - - +
57K VAL* 4.7 5.4 - - + -
87K ILE* 4.6 2.9 - - + -
96K GLN* 3.4 4.6 - - - -
97K TYR* 2.7 60.3 + - + +
99K ALA* 3.9 17.7 - - + -
130K LEU* 5.3 1.3 - - + -
132K ALA 3.9 3.4 - - - +
133K LEU* 3.9 15.5 - - + -
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Residues in contact with THR 43 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41K ARG 5.1 0.3 + - - -
42K MET* 1.3 74.5 + - - +
44K PRO* 1.3 56.7 - - - +
95K ASN* 3.3 28.3 - - + +
96K GLN* 3.5 22.2 + - + +
130K LEU* 3.6 3.4 - - - -
131K ARG* 2.7 48.1 + - + +
132K ALA* 2.9 32.3 + - + +
306K ASN* 4.8 3.5 + - - +
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Residues in contact with PRO 44 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42K MET* 3.6 10.3 - - + +
43K THR* 1.3 87.1 - - - +
45K GLN* 1.3 63.0 + - - +
46K PRO 3.8 0.2 - - - -
48K VAL* 3.6 24.7 - - + +
50K PRO* 4.4 4.7 - - + -
53K CYS* 3.9 29.2 - - + -
95K ASN* 2.9 46.1 + - - +
97K TYR* 3.9 22.0 - - + -
129K ALA 4.0 5.2 - - - +
131K ARG* 3.9 4.3 - - - +
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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