Contacts of the strand formed by residues 107 - 116 (chain I) in PDB entry 5LN3
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 MET 107 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102I LEU 5.3 1.3 - - - +
103I ARG* 3.0 42.0 - - - +
104I GLY 4.4 0.4 - - - +
105I THR* 3.8 13.0 - - - -
106I PRO* 1.3 79.8 - - - +
108I SER* 1.3 59.3 + - - +
151I LEU* 4.6 13.9 - - + -
152I LEU 3.9 7.2 - - - +
153I ASN* 5.1 2.7 - - - +
160I ILE* 4.5 16.8 - - + -
84J LYS* 3.9 25.4 - - + -
95J PHE* 3.3 5.7 - - - -
96J VAL* 2.9 70.0 + - + +
97J VAL* 4.4 1.8 - - - +
98J ASP 5.1 0.2 - - - +
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Residues in contact with SER 108 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106I PRO* 4.3 0.8 - - - +
107I MET* 1.3 72.2 - - - +
109I VAL* 1.3 72.5 + - - +
127I VAL* 4.2 22.3 - - - +
151I LEU* 3.3 5.6 - - - -
152I LEU* 2.7 42.9 + - - -
153I ASN* 4.9 6.9 - - - +
154I HIS* 5.2 5.3 - - - +
94J LYS 4.3 1.7 + - - -
95J PHE* 3.5 29.3 - - - -
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Residues in contact with VAL 109 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108I SER* 1.3 89.3 + - - +
110I GLY* 1.4 72.1 - - - +
127I VAL* 5.6 1.9 - - - +
149I SER* 4.2 15.3 - - - +
150I VAL 3.6 7.9 - - - +
151I LEU* 3.7 18.4 - - + -
152I LEU* 5.1 1.3 - - - -
163I LEU* 4.2 13.0 - - + -
86J LEU* 4.3 13.2 - - + -
94J LYS* 3.4 54.1 + - + +
95J PHE* 4.5 2.9 - - - +
96J VAL* 4.6 1.8 - - + -
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Residues in contact with GLY 110 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108I SER 3.9 0.4 + - - -
109I VAL* 1.4 79.7 - - - +
111I THR* 1.4 63.9 + - - +
124I SER 5.0 3.6 - - - -
125I THR* 6.2 1.8 - - - -
149I SER* 3.4 5.9 - - - -
150I VAL* 3.0 31.2 + - - +
152I LEU* 4.9 13.5 - - - +
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Residues in contact with THR 111 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110I GLY* 1.4 76.4 - - - +
112I LEU* 1.4 61.7 + - - +
113I GLU* 3.1 19.5 + - - +
123I VAL* 3.8 6.3 - - - +
124I SER* 3.4 34.6 + - - +
147I GLY* 4.3 8.1 - - - +
148I CYS 3.4 13.7 - - - +
149I SER* 3.6 17.9 - - - +
150I VAL* 4.6 4.2 - - - +
152I LEU* 5.5 1.0 - - - +
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Residues in contact with LEU 112 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77H LEU* 4.5 12.3 - - + -
79H ASP* 4.0 8.1 - - - +
111I THR* 1.4 71.0 - - - +
113I GLU* 1.3 60.1 - - - +
114I GLU 3.0 35.2 - - - +
115I ILE* 4.3 6.7 - - + +
121I ALA* 3.9 15.5 - - + -
122I ILE 4.0 4.0 - - - +
123I VAL* 4.2 6.1 - - + -
144I LEU* 3.8 31.2 - - + -
145I GLU 4.1 5.6 - - - +
146I PRO* 5.4 0.4 - - + -
147I GLY* 3.2 26.3 + - - -
148I CYS* 2.9 38.2 + - - +
150I VAL* 4.3 12.5 - - + +
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Residues in contact with GLU 113 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161H VAL* 5.8 7.0 - - + +
111I THR* 3.1 27.5 + - - +
112I LEU* 1.3 73.5 - - - +
114I GLU* 1.3 65.5 + - + +
122I ILE* 2.9 28.1 + - + +
123I VAL 3.9 3.6 - - - -
124I SER* 3.4 38.0 - - - +
146I PRO* 4.2 2.8 - - - +
147I GLY* 3.5 16.6 + - - -
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Residues in contact with GLU 114 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92H PRO* 5.2 3.8 - - - +
139H ARG* 3.8 8.5 + - - -
160H THR* 3.2 32.8 - - - +
161H VAL* 3.5 18.6 - - + +
162H THR* 5.6 0.6 + - - -
112I LEU* 3.0 16.9 - - - +
113I GLU* 1.3 83.1 - - + +
115I ILE* 1.3 60.7 + - - +
116I ILE* 3.5 21.1 - - + +
121I ALA* 3.5 0.3 - - - +
122I ILE* 3.0 43.5 + - + +
146I PRO* 4.4 11.4 - - + -
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Residues in contact with ILE 115 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79H ASP* 3.6 30.5 - - + +
81H ALA* 5.7 1.8 - - + -
112I LEU* 4.3 9.6 - - + -
114I GLU* 1.3 76.9 - - - +
116I ILE* 1.4 68.1 + - - +
117I ASP* 3.2 27.7 + - - +
141I LYS* 5.0 4.5 - - + +
144I LEU* 3.9 17.3 - - + +
145I GLU 3.9 9.0 - - - +
146I PRO* 3.8 40.4 - - + +
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Residues in contact with ILE 116 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79H ASP 3.3 2.0 - - - +
88H GLN* 5.0 10.3 - - - +
91H GLN* 3.7 29.8 - - + +
92H PRO* 4.4 21.1 - - + -
114I GLU* 3.5 31.6 - - + +
115I ILE* 1.4 75.9 - - - +
117I ASP* 1.3 57.9 - - - +
118I ASP* 3.3 3.5 + - + +
120I HIS* 2.6 62.0 + - + +
121I ALA* 3.9 7.5 - - - +
122I ILE* 4.1 20.2 - - + +
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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