Contacts of the strand formed by residues 128 - 138 (chain X) in PDB entry 3EHW
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 128 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39X THR* 4.4 2.0 - - - -
41X GLY* 5.3 1.4 - - - -
49X ASP* 3.0 44.4 + - + -
50X LEU 3.3 6.5 - - - +
51X TYR* 3.6 37.1 + - + -
85X ARG* 3.2 39.5 + - - +
88X LEU* 3.8 8.0 - - - +
126X GLY 3.6 0.4 + - - -
127X ASP* 1.3 68.6 - - - +
129X ILE* 1.3 60.6 + - - +
130X ALA 3.6 1.6 - - - -
161Z THR* 2.9 43.9 + - - -
162Z GLY* 3.2 21.9 - - - -
163Z LYS 2.9 10.8 + - - +
164Z ASN 2.8 29.0 + - - +
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Residues in contact with ILE 129 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50X LEU* 3.0 12.7 + - + +
51X TYR 4.7 0.9 - - - -
52X SER* 4.0 9.9 - - - +
66X VAL* 4.1 18.6 - - + -
68X THR* 5.4 0.4 - - + -
85X ARG* 4.4 4.0 + - - +
88X LEU* 3.8 22.8 - - + +
94X ILE* 5.2 0.7 - - - +
96X VAL* 4.5 2.8 - - - +
111X VAL* 3.8 33.9 - - + -
113X LEU* 3.6 28.6 - - + +
121X PHE* 4.5 5.8 - - + -
123X VAL* 4.0 22.0 - - + -
127X ASP* 3.7 28.9 - - + +
128X ARG* 1.3 77.7 - - - +
130X ALA* 1.3 68.8 + - + +
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Residues in contact with ALA 130 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49X ASP* 3.4 7.1 - - - +
50X LEU* 2.7 32.6 + - + +
82X VAL* 3.6 12.3 - - + -
83X ALA 3.5 14.1 - - - +
85X ARG* 4.0 14.5 - - - +
96X VAL* 4.2 2.9 - - + -
111X VAL* 3.6 28.0 - - + -
128X ARG 3.6 0.8 + - - -
129X ILE* 1.3 87.8 - - + +
131X GLN* 1.3 57.8 + - - +
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Residues in contact with GLN 131 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45X ALA* 5.8 1.4 - - - +
47X GLY* 3.9 19.8 + - - +
48X TYR 3.2 11.9 - - - +
49X ASP* 3.8 15.4 - - - +
50X LEU* 4.2 4.9 - - - +
81X ARG 3.3 1.9 - - - +
82X VAL* 3.4 2.9 - - - -
83X ALA* 2.8 45.6 + - + +
84X PRO 2.9 22.2 + - - -
85X ARG* 4.0 6.1 - - + +
130X ALA* 1.3 78.4 - - - +
132X LEU* 1.3 60.2 + - - +
133X ILE* 3.9 2.2 + - + -
100Y VAL* 3.6 21.2 - - - +
102Y ASP* 5.0 1.6 - - - +
777Z DUP 2.8 38.1 + - - -
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Residues in contact with LEU 132 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26X LEU* 4.0 26.2 - - + -
38X PRO* 6.1 1.8 - - + -
46X ALA 4.1 0.5 - - - +
47X GLY* 3.2 2.1 - - - -
48X TYR* 2.6 42.8 + - + +
50X LEU* 4.1 20.2 - - + -
70X ILE* 5.9 0.2 - - + -
72X ILE* 3.6 35.0 - - + -
74X LEU* 4.6 2.9 - - + -
80X GLY* 3.8 35.0 - - - +
81X ARG 3.5 4.7 - - - +
82X VAL* 4.4 7.2 - - + +
101X ILE* 4.2 8.1 - - + -
109X VAL* 5.5 1.8 - - + -
131X GLN* 1.3 72.5 - - - +
133X ILE* 1.3 61.9 + - - +
134X CYS* 4.1 4.2 + - - +
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Residues in contact with ILE 133 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46X ALA* 3.7 20.9 - - + +
47X GLY* 4.1 7.0 - - - -
80X GLY* 3.3 4.2 - - - -
81X ARG* 2.8 69.5 + - - +
83X ALA* 3.7 17.9 - - + -
131X GLN* 4.7 2.7 - - + -
132X LEU* 1.3 76.5 - - - +
134X CYS* 1.3 62.6 + - - +
135X GLU* 3.1 20.5 + - + +
79Y TYR* 3.7 17.3 - - + +
100Y VAL* 3.8 15.3 - - + -
137Y ILE* 3.5 28.0 - - + -
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Residues in contact with CYS 134 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26X LEU* 4.1 14.4 - - - -
46X ALA 4.5 3.2 + - - -
48X TYR* 5.9 1.6 - - - -
74X LEU* 4.1 15.7 - - - -
75X PRO* 4.3 2.7 - - - -
78X CYS* 3.7 22.9 - - - +
79X TYR 3.5 6.1 - - - -
132X LEU* 4.1 4.8 + - - -
133X ILE* 1.3 71.3 - - - +
135X GLU* 1.3 60.8 + - - +
136X ARG 3.4 0.2 + - - -
137Y ILE* 3.2 10.1 - - - +
138Y PHE* 3.1 43.0 + - + +
140Y PRO* 3.8 25.8 - - - -
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Residues in contact with GLU 135 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78X CYS* 3.0 20.6 - - - -
79X TYR* 3.0 37.4 + - + +
81X ARG* 2.9 39.4 + - + -
133X ILE* 3.7 9.3 - - + +
134X CYS* 1.3 68.3 - - - +
136X ARG* 1.3 62.9 + - - +
137X ILE 3.6 0.7 + - - -
79Y TYR* 2.5 44.9 + - - -
81Y ARG* 5.0 0.2 - - - -
135Y GLU* 3.6 18.9 - - - +
136Y ARG 4.0 3.0 - - - +
137Y ILE* 3.6 2.5 - - - +
135Z GLU* 3.6 10.2 - - - +
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Residues in contact with ARG 136 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77X GLY 3.2 8.5 + - - +
78X CYS* 4.1 0.2 - - - -
135X GLU* 1.3 71.7 - - - +
137X ILE* 1.3 62.3 + - - +
77Y GLY 5.3 1.0 + - - -
136Y ARG* 2.9 50.1 + - + +
137Y ILE 3.7 30.0 + - - +
138Y PHE* 3.4 45.8 - - + +
135Z GLU* 3.9 2.6 - - - +
136Z ARG* 3.0 58.6 + - - +
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Residues in contact with ILE 137 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77X GLY* 2.9 23.7 + - - +
78X CYS* 4.1 8.3 - - - -
79X TYR* 3.5 27.4 - - + +
136X ARG* 1.3 80.2 - - - +
138X PHE* 1.3 68.1 + - - +
139X TYR* 3.5 44.3 - - + +
46Z ALA* 3.9 28.3 - - + +
133Z ILE* 3.5 13.2 - - + -
134Z CYS 3.2 15.7 - - - +
135Z GLU* 3.6 6.1 - - - +
136Z ARG* 3.8 13.8 + - - +
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Residues in contact with PHE 138 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137X ILE* 1.3 85.4 - - - +
139X TYR* 1.3 65.2 + - - +
140X PRO* 3.2 22.3 - - + +
25Z GLN* 5.9 2.7 - - - -
40Z ARG* 4.3 1.7 + - - -
46Z ALA 5.0 1.7 - - - +
75Z PRO* 4.3 13.9 - - + -
76Z SER 3.8 13.7 - - - -
77Z GLY* 4.7 1.3 - - - -
78Z CYS* 2.8 35.7 - - - -
134Z CYS* 3.1 21.1 + - + +
136Z ARG* 3.3 43.5 - - + +
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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