Contacts of the strand formed by residues 103 - 114 (chain A) in PDB entry 4MT5
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 GLN 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A TYR* 3.6 36.2 + - + +
101A THR* 3.8 13.3 - - - +
102A VAL* 1.3 93.5 + - + +
104A PRO* 1.4 81.6 - - + +
105A ASP* 3.6 2.6 + - - +
149A PRO* 3.1 34.9 - - + +
150A ALA 4.8 2.9 + - - +
151A VAL* 3.7 27.5 - - + +
179A TYR* 4.7 2.7 - - - +
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Residues in contact with PRO 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A TYR* 3.3 13.3 - - - -
101A THR* 4.7 5.8 - - + -
103A GLN* 1.4 100.7 - - + +
105A ASP* 1.3 70.5 + - - +
149A PRO* 6.0 0.2 - - - +
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Residues in contact with ASP 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A THR* 4.1 7.4 - - + +
92A ILE 2.8 20.2 - - - +
93A HIS* 2.9 45.0 + - - +
94A TYR* 4.0 3.4 + - - -
101A THR* 5.9 0.2 - - - +
103A GLN 3.6 1.8 + - - +
104A PRO* 1.3 77.3 - - - +
106A SER* 1.3 64.0 + - - +
107A THR* 3.8 7.5 + - - +
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Residues in contact with SER 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A GLU* 3.6 2.1 + - - +
91A THR* 3.4 4.2 - - - +
92A ILE* 2.8 47.0 + - - +
94A TYR* 3.8 23.4 - - - -
104A PRO 3.6 2.2 + - - -
105A ASP* 1.3 72.3 - - - +
107A THR* 1.3 61.7 + - - +
108A THR* 4.5 8.8 - - - +
146A VAL* 4.0 22.0 - - - +
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Residues in contact with THR 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A THR* 5.3 4.3 - - - -
90A GLU 3.3 11.4 + - - -
91A THR* 3.6 15.4 + - - +
105A ASP* 3.8 8.1 + - - +
106A SER* 1.3 76.2 + - - +
108A THR* 1.3 69.9 + - - +
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Residues in contact with THR 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A THR* 3.5 2.7 - - - -
90A GLU* 2.9 53.2 + - - +
106A SER* 4.3 11.6 - - - +
107A THR* 1.3 82.6 + - - +
109A ALA* 1.3 60.4 + - - +
143A PHE* 3.5 22.7 - - - -
146A VAL* 5.5 6.3 - - + -
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Residues in contact with ALA 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A THR* 4.6 6.3 - - + -
88A VAL 3.8 3.8 - - - -
89A THR* 3.5 22.0 - - + -
108A THR* 1.3 76.5 - - - +
110A VAL* 1.3 62.3 + - - +
111A THR* 4.3 1.6 - - - +
143A PHE* 4.4 3.7 - - - -
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Residues in contact with VAL 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A LYS 3.9 1.0 - - - +
87A THR* 3.4 3.1 - - - +
88A VAL* 2.8 49.5 + - + +
109A ALA* 1.3 74.8 - - - +
111A THR* 1.3 65.2 + - - +
112A PHE* 4.0 28.1 - - + -
133A VAL* 4.0 26.0 - - + -
141A LYS* 4.0 22.2 - - + +
143A PHE* 3.7 17.9 - - + -
166A VAL* 4.1 11.4 - - + -
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Residues in contact with THR 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A GLN* 4.4 12.8 - - + +
86A LYS 3.6 3.4 - - - +
87A THR* 2.8 25.3 + - - +
109A ALA* 5.6 2.1 - - - +
110A VAL* 1.3 76.4 - - - +
112A PHE* 1.3 72.5 + - - +
113A LYS* 3.9 29.4 + - + +
132A THR 4.0 5.5 - - - +
133A VAL* 4.1 12.4 - - - +
134A ASP* 4.5 3.6 + - - +
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Residues in contact with PHE 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A GLU 3.8 0.3 - - - +
85A GLN* 3.2 5.0 - - - -
86A LYS* 2.8 43.0 + - + +
88A VAL* 4.6 4.3 - - + -
110A VAL* 4.0 21.8 - - + -
111A THR* 1.3 75.3 - - - +
113A LYS* 1.3 60.7 + - - +
131A TRP* 3.8 20.4 - - + -
132A THR 3.6 2.9 - - - -
133A VAL* 3.4 25.4 - - + -
138A ALA 4.3 7.2 - - - -
139A ASP 4.1 0.4 - - - -
140A SER* 3.9 26.2 - - - -
141A LYS* 4.2 8.7 - - + -
166A VAL* 3.6 24.2 - - + -
167A THR 3.8 16.8 - - - -
168A PRO* 3.7 28.5 - - + -
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Residues in contact with LYS 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ALA* 3.9 24.2 + - + +
79A THR* 6.0 1.4 - - - +
80A ASP 5.9 0.4 - - - -
83A ALA* 5.1 0.2 - - + -
84A GLU 3.3 5.2 - - - +
85A GLN* 3.7 39.3 - - + +
111A THR* 3.9 16.0 + - + +
112A PHE* 1.3 79.1 - - - +
114A ARG* 1.3 59.2 + - - +
131A TRP* 3.7 2.2 - - - -
132A THR* 2.7 51.0 + - - +
134A ASP 6.1 2.9 - - - +
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Residues in contact with ARG 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ALA* 4.0 10.7 - - - +
83A ALA* 3.6 3.6 - - - +
84A GLU* 2.9 63.9 + - + +
113A LYS* 1.3 75.8 - - - +
115A GLY* 1.3 63.4 + - - +
116A TYR* 4.1 0.9 - - + -
128A TYR* 3.2 45.6 - - + +
129A ASP 3.7 23.6 + - - +
130A PRO 3.9 8.5 - - - +
131A TRP* 3.5 51.0 - - + +
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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