Contacts of the strand formed by residues 97 - 103 (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 TYR 97 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40K PHE 3.3 0.9 - - - +
41K ARG* 3.4 3.1 - - - +
42K MET* 2.7 47.8 + - + +
44K PRO* 3.9 28.3 - - + -
50K PRO* 3.9 34.5 - - + +
87K ILE* 3.8 24.2 - - + -
88K GLU 3.2 7.2 - - - +
89K PRO* 4.1 21.3 - - + -
90K VAL* 3.9 4.0 - - - -
94K ASP 4.0 14.2 + - - -
95K ASN* 4.0 21.8 + - - -
96K GLN* 1.3 80.3 - - - +
98K ILE* 1.3 61.8 + - - +
99K ALA 3.8 0.2 - - - -
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Residues in contact with ILE 98 (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* 4.1 18.4 - - + -
40K PHE 3.2 6.7 - - - +
41K ARG* 3.9 31.0 - - + +
87K ILE* 3.3 3.5 - - - -
88K GLU* 2.7 57.4 + - + +
89K PRO 5.5 0.7 - - - +
90K VAL* 3.9 21.5 - - + +
97K TYR* 1.3 71.9 - - - +
99K ALA* 1.3 62.7 + - - +
100K TYR* 3.6 31.3 - - + +
136K GLU* 4.9 0.9 - - + -
358K ARG* 4.3 10.8 - - - +
363K TYR* 4.1 20.0 - - + +
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Residues in contact with ALA 99 (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 3.6 1.9 - - - +
40K PHE* 2.8 46.0 + - + +
42K MET* 3.9 33.7 - - + -
54K GLY* 4.3 3.4 - - - -
57K VAL* 6.1 1.6 - - + -
84K CYS* 4.2 17.0 - - - -
86K ASP 3.6 4.3 - - - -
87K ILE* 4.5 3.6 - - + -
97K TYR 3.8 1.4 + - - -
98K ILE* 1.3 73.2 - - - +
100K TYR* 1.3 62.0 + - - +
101K VAL* 4.0 4.3 + - + -
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Residues in contact with TYR 100 (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 3.4 3.8 - - - -
39K ALA* 3.9 18.2 - - + -
84K CYS* 3.2 6.1 - - - -
85K TYR* 2.9 52.5 + + + -
86K ASP* 2.8 35.5 + - + +
88K GLU* 3.0 41.9 + - + -
98K ILE* 3.6 26.6 - - + +
99K ALA* 1.3 72.6 - - - +
101K VAL* 1.3 60.9 + - - +
356K LYS* 5.5 3.2 + - - -
358K ARG* 3.4 12.1 + - - -
363K TYR* 3.8 11.7 + + + +
364K PHE* 3.8 31.4 - + - -
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Residues in contact with VAL 101 (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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36K ILE 3.8 0.9 - - - +
37K LEU* 3.3 4.9 - - - -
38K ALA 2.9 32.5 + - - +
40K PHE* 4.0 26.2 - - + -
54K GLY 4.7 1.6 - - - +
57K VAL* 4.6 2.5 - - + -
58K ALA* 3.8 33.2 - - + +
83K ARG 3.2 14.1 - - - +
84K CYS* 4.3 6.7 - - + -
85K TYR* 3.6 3.4 - - - -
99K ALA* 4.5 4.7 - - + +
100K TYR* 1.3 79.3 - - - +
102K ALA* 1.3 64.0 + - - +
103K TYR* 3.5 37.9 - - + +
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Residues in contact with ALA 102 (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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29K TYR* 3.7 26.7 - - + -
31K VAL* 4.2 0.9 - - + -
35K ASP* 4.0 5.8 - - - +
36K ILE 3.5 3.6 - - - -
37K LEU* 3.8 15.9 - - + -
81K LYS 4.2 0.2 - - - +
82K GLY* 3.3 4.9 - - - -
83K ARG* 2.8 35.7 + - + +
85K TYR* 3.6 17.4 - - + -
101K VAL* 1.3 73.9 - - - +
103K TYR* 1.3 62.0 + - - +
104K HYP 3.9 3.8 - - - -
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Residues in contact with TYR 103 (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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35K ASP* 3.3 5.6 - - - -
36K ILE* 2.8 48.1 + - + +
38K ALA* 3.8 21.1 - - + -
40K PHE* 3.6 22.5 - - - -
58K ALA 4.6 0.4 - - - -
61K SER* 2.7 51.0 + - - -
62K SER* 4.3 6.7 - - - -
82K GLY* 4.5 3.6 - - - -
101K VAL* 3.5 23.7 - - + +
102K ALA* 1.3 74.2 - - - +
104K HYP 1.3 68.1 + - + +
107K LEU* 4.2 13.5 - - + -
108K PHE* 3.5 26.5 - + + -
119K SER* 5.6 0.4 - - - -
120K ILE* 3.9 25.4 - - + +
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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