Contacts of the strand formed by residues 109 - 118 (chain H) in PDB entry 1MWA
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 LEU 109 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101H CYS* 3.5 22.2 - - + -
102H GLU 3.8 6.1 - - - +
103H VAL* 4.2 3.4 - - + -
107H GLY 3.9 1.2 + - - -
108H ARG* 1.3 82.7 - - - +
110H LEU* 1.3 60.7 + - - +
111H ARG* 3.3 31.0 - - - +
112H GLY* 4.5 1.8 - - - +
130H LEU* 4.1 16.6 - - + -
160H LEU 3.8 4.5 - - - +
161H GLU* 3.7 38.6 - - + +
165H VAL* 3.7 19.3 - - + +
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Residues in contact with LEU 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2H PRO* 3.9 21.1 - - + -
102H GLU* 2.6 20.4 + - + +
103H VAL 3.9 1.8 - - - -
104H GLY* 3.7 34.8 - - - +
106H ASP* 5.8 1.3 - - - +
108H ARG* 3.3 8.5 + - + +
109H LEU* 1.3 75.0 - - - +
111H ARG* 1.3 69.9 + - + +
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Residues in contact with ARG 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H ARG* 5.1 0.4 - - - +
101H CYS* 3.2 4.7 - - - -
102H GLU* 2.7 72.1 + - - +
109H LEU* 3.3 11.1 - - - +
110H LEU* 1.3 89.2 - - + +
112H GLY* 1.3 62.9 + - - +
113H TYR* 3.2 39.7 - - - +
115H GLN* 5.1 4.9 + - - -
128H GLU* 3.1 36.5 + - - +
58L LYS* 5.6 6.3 - - - +
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Residues in contact with GLY 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100H GLY 3.4 8.1 - - - -
101H CYS* 4.4 1.1 - - - -
109H LEU* 4.5 5.9 - - - +
111H ARG* 1.3 80.4 + - - +
113H TYR* 1.3 65.0 + - - +
126H LEU* 4.5 5.0 - - - +
127H ASN 4.9 0.3 - - - +
128H GLU* 5.2 3.1 - - - +
130H LEU* 3.4 31.3 - - - +
160H LEU* 4.3 14.6 - - - -
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Residues in contact with TYR 113 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H ARG* 2.4 47.3 + - - +
98H ILE* 4.0 27.6 - - + -
99H SER* 3.1 4.0 - - - -
100H GLY 2.9 56.1 + - - -
101H CYS 3.8 3.3 + - - -
102H GLU* 3.4 25.4 - - + +
111H ARG* 3.2 34.3 - - - +
112H GLY* 1.3 80.0 - - - +
114H GLN* 1.3 61.2 + - - +
115H GLN* 4.7 18.8 - - + +
126H LEU* 4.9 10.8 - - - +
160H LEU* 3.9 7.2 - - - +
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Residues in contact with GLN 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97H VAL* 4.2 2.0 - - + -
98H ILE 3.2 4.3 - - - -
99H SER* 3.2 25.2 + - - -
113H TYR* 1.3 74.6 - - - +
115H GLN* 1.3 62.5 + - - +
116H TYR* 3.9 25.1 + - + -
125H ALA* 3.4 3.1 - - - -
126H LEU* 3.1 30.1 + - + +
133H TRP* 4.9 4.6 - - + -
147H TRP* 5.1 5.3 - - - -
152H GLU* 4.9 2.0 + - - -
156H LEU* 3.6 46.7 - - + +
3P TYR* 4.0 11.0 - - - -
5P PHE* 3.3 30.6 - - - +
6P TYR 6.0 0.6 - - - +
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Residues in contact with GLN 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97H VAL* 3.0 8.1 - - - +
98H ILE* 2.8 51.0 + - - +
111H ARG* 5.1 5.0 + - - -
113H TYR* 4.7 18.9 - - + +
114H GLN* 1.3 82.1 - - - +
116H TYR* 1.3 62.9 + - - +
122H ASP* 5.9 0.2 - - - +
124H ILE 3.8 4.0 - - - -
125H ALA* 4.2 14.1 - - + -
58L LYS* 5.0 14.9 + - - +
60L TRP* 3.6 25.9 - - + -
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Residues in contact with TYR 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74H PHE* 3.8 23.6 - + - -
77H SER* 5.8 2.0 - - - -
95H ILE* 4.1 18.4 - - + -
96H GLN 3.4 2.7 - - - -
97H VAL* 4.0 12.1 - - + -
114H GLN* 3.9 25.1 + - + -
115H GLN* 1.3 81.4 - - - +
117H ALA* 1.3 62.5 + - - +
122H ASP* 3.5 5.9 - - - +
123H TYR* 2.8 26.4 + + + -
124H ILE* 2.9 41.0 + - + +
147H TRP* 3.5 29.9 - + - -
60L TRP* 3.9 4.6 - - - -
5P PHE* 3.5 25.3 - - - +
6P TYR 4.5 3.5 + - - -
7P SER* 5.9 0.3 - - - -
8P VAL* 4.5 16.8 - - + -
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Residues in contact with ALA 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94H THR 3.8 0.2 - - - +
95H ILE* 3.3 7.6 - - - +
96H GLN* 2.8 35.7 + - + +
116H TYR* 1.3 76.7 - - - +
118H TYR* 1.3 61.1 + - - +
120H GLY 4.9 0.4 - - - -
121H CYS 3.3 18.2 - - - +
123H TYR* 3.8 3.4 - - - +
60L TRP* 3.3 46.2 - - + +
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Residues in contact with TYR 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78H LEU* 4.9 4.5 + - + -
81H LEU* 3.5 37.6 - - + +
82H LEU* 4.1 5.7 - - - +
85H TYR* 3.7 35.0 - + - +
87H GLN* 2.5 37.5 + - - -
93H HIS* 2.8 40.0 + - + +
94H THR 3.1 15.5 - - - -
95H ILE* 4.1 3.6 - - + -
117H ALA* 1.3 73.9 - - - +
119H ASP* 1.3 77.5 + - + +
120H GLY 3.2 0.7 - - - -
121H CYS* 2.9 25.2 + - - +
123H TYR* 4.2 14.1 - - + +
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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