Contacts of the strand formed by residues 103 - 117 (chain L) in PDB entry 1M4U
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 CYS 103 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69L GLY 5.6 0.4 - - - -
71L CYS* 3.8 4.5 - - - -
101L LYS 5.1 0.9 - - - +
102L PRO* 1.3 75.1 - - - +
104L CYS* 1.3 63.2 - - - +
105L ALA* 3.4 17.3 + - - -
137L GLY 3.3 0.7 - - - +
138L CYS* 3.5 0.3 - - - -
139L HIS* 2.9 36.6 + - - -
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Residues in contact with CYS 104 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38L CYS* 2.0 50.9 - - + -
39L LYS 3.6 7.9 - - - -
67L CYS* 3.7 18.8 - - - +
68L GLU* 3.6 18.6 - - - -
69L GLY 3.4 27.0 + - - +
71L CYS* 3.7 4.6 - - - -
103L CYS* 1.3 73.8 - - - +
105L ALA* 1.3 59.2 + - - +
136L CYS* 4.1 1.8 - - - -
137L GLY 3.4 5.6 - - - -
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Residues in contact with ALA 105 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67L CYS* 3.5 6.5 - - - -
103L CYS* 4.2 13.0 - - - -
104L CYS* 1.3 76.4 - - - +
106L PRO* 1.3 76.3 - - + +
136L CYS* 3.4 0.3 - - - -
137L GLY 2.8 22.0 + - - -
139L HIS* 2.6 36.1 + - + +
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Residues in contact with PRO 106 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67L CYS* 3.3 12.3 - - + +
105L ALA* 1.3 88.5 - - + +
107L THR* 1.3 58.9 + - - +
108L GLN 4.6 0.4 - - - +
109L LEU* 4.1 24.6 - - + +
133L VAL* 3.7 30.1 - - + -
135L ALA 3.3 10.1 - - - +
139L HIS* 3.2 14.9 - - - -
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Residues in contact with THR 107 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80L ASN* 4.2 17.8 + - + +
105L ALA 3.3 0.6 + - - -
106L PRO* 1.3 72.1 - - - +
108L GLN* 1.3 66.6 + - - +
109L LEU* 5.5 1.8 - - - -
135L ALA* 2.7 37.5 + - - +
136L CYS 3.4 4.7 + - - +
137L GLY* 3.9 18.2 - - - +
139L HIS* 3.8 20.6 - - + -
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Residues in contact with GLN 108 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B NAG 3.9 17.8 + - - -
106L PRO* 3.6 0.6 - - - +
107L THR* 1.3 89.1 + - - +
109L LEU* 1.3 63.0 + - - +
110L ASN* 6.1 0.4 - - - +
133L VAL* 3.7 1.4 - - - -
134L ARG* 2.7 52.0 + - + +
135L ALA* 3.3 25.7 + - + +
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Residues in contact with LEU 109 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106L PRO* 4.1 18.8 - - + +
107L THR 5.5 0.4 - - - -
108L GLN* 1.3 80.0 - - - +
110L ASN* 1.3 69.9 + - - +
130L ASN* 3.2 53.7 + - + +
131L MET 4.8 0.7 - - - -
132L VAL 2.7 21.3 - - - +
133L VAL* 3.8 25.1 - - + -
134L ARG* 4.3 1.3 - - - +
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Residues in contact with ASN 110 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108L GLN* 6.1 0.6 - - - +
109L LEU* 1.3 82.2 + - - +
111L ALA* 1.3 68.8 + - - +
130L ASN 4.2 4.0 - - - -
131L MET* 3.0 9.3 + - - -
132L VAL* 2.6 42.7 + - + +
134L ARG* 2.7 49.9 + - - +
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Residues in contact with ALA 111 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110L ASN* 1.3 81.7 - - - +
112L ILE* 1.3 67.9 + - - +
127L LYS* 3.6 32.1 - - + +
128L TYR 3.1 17.5 - - - +
129L ARG* 3.8 10.5 - - + +
130L ASN 4.4 0.4 - - - +
132L VAL* 4.7 0.5 - - - +
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Residues in contact with ILE 112 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47L PHE* 4.5 9.4 - - + -
59L PRO* 4.9 8.7 - - + -
62L TYR* 3.8 38.8 - - + -
111L ALA* 1.3 78.0 - - - +
113L SER* 1.3 73.2 + - - +
114L VAL* 4.4 11.4 - - + -
127L LYS* 3.7 3.1 - - - +
128L TYR* 3.0 25.8 + - - +
131L MET* 4.1 23.5 - - + +
132L VAL* 3.7 26.2 - - + -
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Residues in contact with SER 113 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59L PRO* 3.8 14.2 - - - +
112L ILE* 1.3 79.2 + - - +
114L VAL* 1.3 64.5 + - - +
125L LEU* 4.6 16.8 - - - -
126L LYS 3.3 10.1 - - - -
127L LYS* 4.2 12.1 + - - +
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Residues in contact with VAL 114 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47L PHE* 5.8 1.3 - - + -
56L ILE* 4.1 23.3 - - + -
58L ALA 3.6 9.4 - - - +
59L PRO* 4.3 5.2 - - + -
112L ILE* 4.2 12.1 - - + +
113L SER* 1.3 80.3 - - - +
115L LEU* 1.3 67.3 + - - +
116L TYR* 3.6 23.9 - - + -
125L LEU* 3.4 6.7 - - - +
126L LYS 2.7 30.9 + - - +
128L TYR* 2.8 47.8 - - + -
131L MET* 5.7 1.6 - - + -
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Residues in contact with LEU 115 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56L ILE* 3.5 2.4 - - - +
57L ILE* 2.9 55.3 + - + -
58L ALA* 2.8 31.0 + - + +
114L VAL* 1.3 69.6 - - - +
116L TYR* 1.3 61.6 + - - +
123L VAL* 3.6 21.8 - - + -
124L ILE* 3.6 11.2 - - - +
125L LEU* 3.7 25.5 - - + +
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Residues in contact with TYR 116 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55L TRP* 3.0 36.3 - - - +
56L ILE* 4.0 3.4 - - + +
57L ILE* 4.4 2.0 - - - +
114L VAL* 3.6 23.8 - - + -
115L LEU* 1.3 74.8 - - - +
117L PHE* 1.3 80.8 + - - +
118L ASP* 3.5 19.3 + - + +
123L VAL* 4.1 6.3 - - - -
124L ILE* 2.9 51.7 + - + +
126L LYS* 3.4 36.1 - - + +
128L TYR* 3.6 30.9 + + - -
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Residues in contact with PHE 117 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54L ASP* 3.9 24.5 - - - +
55L TRP* 2.9 27.8 + - + +
57L ILE* 3.8 23.6 - - + -
116L TYR* 1.3 83.2 - - - +
118L ASP* 1.3 63.9 + - - +
121L SER* 4.4 23.6 - - - -
122L ASN 3.3 5.8 - - - -
123L VAL* 3.5 22.7 - - + +
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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